data_3VYB # _entry.id 3VYB # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.381 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3VYB pdb_00003vyb 10.2210/pdb3vyb/pdb NDB NA2057 ? ? RCSB RCSB095652 ? ? WWPDB D_1000095652 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3VXV . unspecified PDB 3VXX . unspecified PDB 3VYQ . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3VYB _pdbx_database_status.recvd_initial_deposition_date 2012-09-22 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Otani, J.' 1 'Arita, K.' 2 'Kato, T.' 3 'Kinoshita, M.' 4 'Ariyoshi, M.' 5 'Shirakawa, M.' 6 # _citation.id primary _citation.title 'Structural basis of the versatile DNA recognition ability of the methyl-CpG binding domain of methyl-CpG binding domain protein 4' _citation.journal_abbrev J.Biol.Chem. _citation.journal_volume 288 _citation.page_first 6351 _citation.page_last 6362 _citation.year 2013 _citation.journal_id_ASTM JBCHA3 _citation.country US _citation.journal_id_ISSN 0021-9258 _citation.journal_id_CSD 0071 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23316048 _citation.pdbx_database_id_DOI 10.1074/jbc.M112.431098 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Otani, J.' 1 ? primary 'Arita, K.' 2 ? primary 'Kato, T.' 3 ? primary 'Kinoshita, M.' 4 ? primary 'Kimura, H.' 5 ? primary 'Suetake, I.' 6 ? primary 'Tajima, S.' 7 ? primary 'Ariyoshi, M.' 8 ? primary 'Shirakawa, M.' 9 ? # _cell.entry_id 3VYB _cell.length_a 88.693 _cell.length_b 97.758 _cell.length_c 55.725 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3VYB _symmetry.space_group_name_H-M 'C 2 2 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'Methyl-CpG-binding domain protein 4' 7829.089 1 3.2.2.- ? 'methyl CpG binding domain, UNP residues 69-136' ? 2 polymer syn ;DNA (5'-D(*GP*TP*CP*AP*CP*TP*AP*CP*(5CM)P*GP*GP*AP*CP*A)-3') ; 4263.809 1 ? ? ? ? 3 polymer syn ;DNA (5'-D(*GP*TP*CP*(5HC)P*GP*GP*TP*AP*GP*TP*GP*AP*CP*T)-3') ; 4341.827 1 ? ? ? ? 4 non-polymer syn 'ACETATE ION' 59.044 1 ? ? ? ? 5 non-polymer syn 1,2-ETHANEDIOL 62.068 1 ? ? ? ? 6 water nat water 18.015 71 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Methyl-CpG-binding protein MBD4, Mismatch-specific DNA N-glycosylase' # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no no SGHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFNFTVLPKG SGHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFNFTVLPKG A ? 2 polydeoxyribonucleotide no yes '(DG)(DT)(DC)(DA)(DC)(DT)(DA)(DC)(5CM)(DG)(DG)(DA)(DC)(DA)' GTCACTACCGGACA B ? 3 polydeoxyribonucleotide no yes '(DG)(DT)(DC)(5HC)(DG)(DG)(DT)(DA)(DG)(DT)(DG)(DA)(DC)(DT)' GTCXGGTAGTGACT C ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 SER n 1 2 GLY n 1 3 HIS n 1 4 LYS n 1 5 PRO n 1 6 VAL n 1 7 PRO n 1 8 CYS n 1 9 GLY n 1 10 TRP n 1 11 GLU n 1 12 ARG n 1 13 VAL n 1 14 VAL n 1 15 LYS n 1 16 GLN n 1 17 ARG n 1 18 LEU n 1 19 SER n 1 20 GLY n 1 21 LYS n 1 22 THR n 1 23 ALA n 1 24 GLY n 1 25 LYS n 1 26 PHE n 1 27 ASP n 1 28 VAL n 1 29 TYR n 1 30 PHE n 1 31 ILE n 1 32 SER n 1 33 PRO n 1 34 GLN n 1 35 GLY n 1 36 LEU n 1 37 LYS n 1 38 PHE n 1 39 ARG n 1 40 SER n 1 41 LYS n 1 42 ARG n 1 43 SER n 1 44 LEU n 1 45 ALA n 1 46 ASN n 1 47 TYR n 1 48 LEU n 1 49 LEU n 1 50 LYS n 1 51 ASN n 1 52 GLY n 1 53 GLU n 1 54 THR n 1 55 PHE n 1 56 LEU n 1 57 LYS n 1 58 PRO n 1 59 GLU n 1 60 ASP n 1 61 PHE n 1 62 ASN n 1 63 PHE n 1 64 THR n 1 65 VAL n 1 66 LEU n 1 67 PRO n 1 68 LYS n 1 69 GLY n 2 1 DG n 2 2 DT n 2 3 DC n 2 4 DA n 2 5 DC n 2 6 DT n 2 7 DA n 2 8 DC n 2 9 5CM n 2 10 DG n 2 11 DG n 2 12 DA n 2 13 DC n 2 14 DA n 3 1 DG n 3 2 DT n 3 3 DC n 3 4 5HC n 3 5 DG n 3 6 DG n 3 7 DT n 3 8 DA n 3 9 DG n 3 10 DT n 3 11 DG n 3 12 DA n 3 13 DC n 3 14 DT n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name mouse _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene Mbd4 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Mus musculus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 10090 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'BL21(DE3)' _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_isoform 1 UNP MBD4_MOUSE Q9Z2D7 1 GHKPVPCGWERVVKQRLSGKTAGKFDVYFISPQGLKFRSKRSLANYLLKNGETFLKPEDFNFTVLPKG 69 ? 2 PDB 3VYB 3VYB 2 ? ? ? 3 PDB 3VYB 3VYB 3 ? ? ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 3VYB A 2 ? 69 ? Q9Z2D7 69 ? 136 ? 69 136 2 2 3VYB B 1 ? 14 ? 3VYB 1 ? 14 ? 1 14 3 3 3VYB C 1 ? 14 ? 3VYB 1 ? 14 ? 1 14 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 3VYB _struct_ref_seq_dif.mon_id SER _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 1 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code Q9Z2D7 _struct_ref_seq_dif.db_mon_id ? _struct_ref_seq_dif.pdbx_seq_db_seq_num ? _struct_ref_seq_dif.details 'expression tag' _struct_ref_seq_dif.pdbx_auth_seq_num 68 _struct_ref_seq_dif.pdbx_ordinal 1 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight 5CM 'DNA linking' n "5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C10 H16 N3 O7 P' 321.224 5HC 'DNA linking' n ;2'-deoxy-5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate) ; ? 'C10 H16 N3 O8 P' 337.223 ACT non-polymer . 'ACETATE ION' ? 'C2 H3 O2 -1' 59.044 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 EDO non-polymer . 1,2-ETHANEDIOL 'ETHYLENE GLYCOL' 'C2 H6 O2' 62.068 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 3VYB _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.67 _exptl_crystal.density_percent_sol 66.53 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 4 _exptl_crystal_grow.pdbx_details '8% PEG 1500, 0.1M sodium acetate, 0.1M sodium cacodylate, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 95 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315r' _diffrn_detector.pdbx_collection_date 2010-10-08 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'PHOTON FACTORY BEAMLINE BL-17A' _diffrn_source.pdbx_synchrotron_site 'Photon Factory' _diffrn_source.pdbx_synchrotron_beamline BL-17A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.0 # _reflns.entry_id 3VYB _reflns.observed_criterion_sigma_I 1.0 _reflns.observed_criterion_sigma_F 1.0 _reflns.d_resolution_low 50 _reflns.d_resolution_high 2.19 _reflns.number_obs 11517 _reflns.number_all ? _reflns.percent_possible_obs 89.6 _reflns.pdbx_Rmerge_I_obs 0.052 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 14.7 _reflns.B_iso_Wilson_estimate 48.250 _reflns.pdbx_redundancy 6.5 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.19 _reflns_shell.d_res_low 2.27 _reflns_shell.percent_possible_all 54.7 _reflns_shell.Rmerge_I_obs 0.317 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy 4.1 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 701 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.number_possible ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.meanI_over_sigI_all ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3VYB _refine.ls_number_reflns_obs 9351 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.00 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 34.700 _refine.ls_d_res_high 2.400 _refine.ls_percent_reflns_obs 95.52 _refine.ls_R_factor_obs 0.1924 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1906 _refine.ls_R_factor_R_free 0.2199 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.88 _refine.ls_number_reflns_R_free 456 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 47.8984 _refine.aniso_B[1][1] -11.0243 _refine.aniso_B[2][2] 8.1093 _refine.aniso_B[3][3] 2.9149 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_ksol 0.329 _refine.solvent_model_param_bsol 39.965 _refine.pdbx_solvent_vdw_probe_radii 1.00 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.72 _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model 'PDB ENTRY 3VXV' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.43 _refine.B_iso_max 100.750 _refine.B_iso_min 22.030 _refine.pdbx_overall_phase_error 24.3500 _refine.occupancy_max 1.000 _refine.occupancy_min 0.500 _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 511 _refine_hist.pdbx_number_atoms_nucleic_acid 571 _refine_hist.pdbx_number_atoms_ligand 8 _refine_hist.number_atoms_solvent 71 _refine_hist.number_atoms_total 1161 _refine_hist.d_res_high 2.400 _refine_hist.d_res_low 34.700 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id f_bond_d 0.004 ? ? 1171 ? 'X-RAY DIFFRACTION' f_angle_d 1.008 ? ? 1694 ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 26.872 ? ? 475 ? 'X-RAY DIFFRACTION' f_chiral_restr 0.056 ? ? 182 ? 'X-RAY DIFFRACTION' f_plane_restr 0.003 ? ? 118 ? 'X-RAY DIFFRACTION' # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_all _refine_ls_shell.R_factor_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs 'X-RAY DIFFRACTION' 3 2.4000 2.7472 2712 0.2838 89.00 0.3224 . . 133 . . . . 'X-RAY DIFFRACTION' 3 2.7472 3.4607 3013 0.1948 99.00 0.2278 . . 170 . . . . 'X-RAY DIFFRACTION' 3 3.4607 34.7032 3170 0.1716 99.00 0.1968 . . 153 . . . . # _struct.entry_id 3VYB _struct.title 'Crystal structure of methyl CpG binding domain of MBD4 in complex with the 5mCG/hmCG sequence' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3VYB _struct_keywords.pdbx_keywords HYDROLASE/DNA _struct_keywords.text 'methyl CpG binding domain, protein-DNA complex, versatile base recognition, HYDROLASE-DNA complex' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 4 ? E N N 5 ? F N N 6 ? G N N 6 ? H N N 6 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 SER A 40 ? GLY A 52 ? SER A 107 GLY A 119 1 ? 13 HELX_P HELX_P2 2 LYS A 57 ? PHE A 61 ? LYS A 124 PHE A 128 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role disulf1 disulf ? ? A CYS 8 SG ? ? ? 1_555 A CYS 8 SG ? ? A CYS 75 A CYS 75 3_555 ? ? ? ? ? ? ? 2.029 ? ? covale1 covale both ? B DC 8 "O3'" ? ? ? 1_555 B 5CM 9 P ? ? B DC 8 B 5CM 9 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale2 covale both ? B 5CM 9 "O3'" ? ? ? 1_555 B DG 10 P ? ? B 5CM 9 B DG 10 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale3 covale both ? C DC 3 "O3'" ? ? ? 1_555 C 5HC 4 P ? ? C DC 3 C 5HC 4 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale4 covale both ? C 5HC 4 "O3'" ? ? ? 1_555 C DG 5 P ? ? C 5HC 4 C DG 5 1_555 ? ? ? ? ? ? ? 1.610 ? ? hydrog1 hydrog ? ? B DG 1 N1 ? ? ? 1_555 C DC 13 N3 ? ? B DG 1 C DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? B DG 1 N2 ? ? ? 1_555 C DC 13 O2 ? ? B DG 1 C DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? B DG 1 O6 ? ? ? 1_555 C DC 13 N4 ? ? B DG 1 C DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? B DT 2 N3 ? ? ? 1_555 C DA 12 N1 ? ? B DT 2 C DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? B DT 2 O4 ? ? ? 1_555 C DA 12 N6 ? ? B DT 2 C DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? B DC 3 N3 ? ? ? 1_555 C DG 11 N1 ? ? B DC 3 C DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? B DC 3 N4 ? ? ? 1_555 C DG 11 O6 ? ? B DC 3 C DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? B DC 3 O2 ? ? ? 1_555 C DG 11 N2 ? ? B DC 3 C DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? B DA 4 N1 ? ? ? 1_555 C DT 10 N3 ? ? B DA 4 C DT 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? B DA 4 N6 ? ? ? 1_555 C DT 10 O4 ? ? B DA 4 C DT 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? B DC 5 N3 ? ? ? 1_555 C DG 9 N1 ? ? B DC 5 C DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? B DC 5 N4 ? ? ? 1_555 C DG 9 O6 ? ? B DC 5 C DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? B DC 5 O2 ? ? ? 1_555 C DG 9 N2 ? ? B DC 5 C DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? B DT 6 N3 ? ? ? 1_555 C DA 8 N1 ? ? B DT 6 C DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? B DT 6 O4 ? ? ? 1_555 C DA 8 N6 ? ? B DT 6 C DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? B DA 7 N1 ? ? ? 1_555 C DT 7 N3 ? ? B DA 7 C DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? B DA 7 N6 ? ? ? 1_555 C DT 7 O4 ? ? B DA 7 C DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? B DC 8 N3 ? ? ? 1_555 C DG 6 N1 ? ? B DC 8 C DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? B DC 8 N4 ? ? ? 1_555 C DG 6 O6 ? ? B DC 8 C DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? B DC 8 O2 ? ? ? 1_555 C DG 6 N2 ? ? B DC 8 C DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? B 5CM 9 N3 ? ? ? 1_555 C DG 5 N1 ? ? B 5CM 9 C DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? B 5CM 9 N4 ? ? ? 1_555 C DG 5 O6 ? ? B 5CM 9 C DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? B 5CM 9 O2 ? ? ? 1_555 C DG 5 N2 ? ? B 5CM 9 C DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? B DG 11 N1 ? ? ? 1_555 C DC 3 N3 ? ? B DG 11 C DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? B DG 11 N2 ? ? ? 1_555 C DC 3 O2 ? ? B DG 11 C DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? B DG 11 O6 ? ? ? 1_555 C DC 3 N4 ? ? B DG 11 C DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? B DA 12 N1 ? ? ? 1_555 C DT 2 N3 ? ? B DA 12 C DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? B DA 12 N6 ? ? ? 1_555 C DT 2 O4 ? ? B DA 12 C DT 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? B DC 13 N3 ? ? ? 1_555 C DG 1 N1 ? ? B DC 13 C DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? B DC 13 N4 ? ? ? 1_555 C DG 1 O6 ? ? B DC 13 C DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B DC 13 O2 ? ? ? 1_555 C DG 1 N2 ? ? B DC 13 C DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? covale ? ? hydrog ? ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 3 _struct_sheet.details ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 GLU A 11 ? GLN A 16 ? GLU A 78 GLN A 83 A 2 PHE A 26 ? ILE A 31 ? PHE A 93 ILE A 98 A 3 LYS A 37 ? PHE A 38 ? LYS A 104 PHE A 105 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 N VAL A 13 ? N VAL A 80 O TYR A 29 ? O TYR A 96 A 2 3 N PHE A 30 ? N PHE A 97 O PHE A 38 ? O PHE A 105 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A ACT 201 ? 4 'BINDING SITE FOR RESIDUE ACT A 201' AC2 Software A EDO 202 ? 6 'BINDING SITE FOR RESIDUE EDO A 202' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 4 GLU A 53 ? GLU A 120 . ? 1_555 ? 2 AC1 4 GLU A 53 ? GLU A 120 . ? 3_555 ? 3 AC1 4 DT C 14 ? DT C 14 . ? 6_555 ? 4 AC1 4 DT C 14 ? DT C 14 . ? 8_455 ? 5 AC2 6 GLN A 16 ? GLN A 83 . ? 1_555 ? 6 AC2 6 ARG A 17 ? ARG A 84 . ? 1_555 ? 7 AC2 6 HOH F . ? HOH A 323 . ? 1_555 ? 8 AC2 6 DC C 3 ? DC C 3 . ? 1_555 ? 9 AC2 6 5HC C 4 ? 5HC C 4 . ? 1_555 ? 10 AC2 6 HOH H . ? HOH C 106 . ? 1_555 ? # _database_PDB_matrix.entry_id 3VYB _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 3VYB _atom_sites.fract_transf_matrix[1][1] 0.011275 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.010229 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.017945 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 SER 1 68 ? ? ? A . n A 1 2 GLY 2 69 ? ? ? A . n A 1 3 HIS 3 70 ? ? ? A . n A 1 4 LYS 4 71 ? ? ? A . n A 1 5 PRO 5 72 72 PRO PRO A . n A 1 6 VAL 6 73 73 VAL VAL A . n A 1 7 PRO 7 74 74 PRO PRO A . n A 1 8 CYS 8 75 75 CYS CYS A . n A 1 9 GLY 9 76 76 GLY GLY A . n A 1 10 TRP 10 77 77 TRP TRP A . n A 1 11 GLU 11 78 78 GLU GLU A . n A 1 12 ARG 12 79 79 ARG ARG A . n A 1 13 VAL 13 80 80 VAL VAL A . n A 1 14 VAL 14 81 81 VAL VAL A . n A 1 15 LYS 15 82 82 LYS LYS A . n A 1 16 GLN 16 83 83 GLN GLN A . n A 1 17 ARG 17 84 84 ARG ARG A . n A 1 18 LEU 18 85 85 LEU LEU A . n A 1 19 SER 19 86 86 SER SER A . n A 1 20 GLY 20 87 87 GLY GLY A . n A 1 21 LYS 21 88 88 LYS LYS A . n A 1 22 THR 22 89 89 THR THR A . n A 1 23 ALA 23 90 90 ALA ALA A . n A 1 24 GLY 24 91 91 GLY GLY A . n A 1 25 LYS 25 92 92 LYS LYS A . n A 1 26 PHE 26 93 93 PHE PHE A . n A 1 27 ASP 27 94 94 ASP ASP A . n A 1 28 VAL 28 95 95 VAL VAL A . n A 1 29 TYR 29 96 96 TYR TYR A . n A 1 30 PHE 30 97 97 PHE PHE A . n A 1 31 ILE 31 98 98 ILE ILE A . n A 1 32 SER 32 99 99 SER SER A . n A 1 33 PRO 33 100 100 PRO PRO A . n A 1 34 GLN 34 101 101 GLN GLN A . n A 1 35 GLY 35 102 102 GLY GLY A . n A 1 36 LEU 36 103 103 LEU LEU A . n A 1 37 LYS 37 104 104 LYS LYS A . n A 1 38 PHE 38 105 105 PHE PHE A . n A 1 39 ARG 39 106 106 ARG ARG A . n A 1 40 SER 40 107 107 SER SER A . n A 1 41 LYS 41 108 108 LYS LYS A . n A 1 42 ARG 42 109 109 ARG ARG A . n A 1 43 SER 43 110 110 SER SER A . n A 1 44 LEU 44 111 111 LEU LEU A . n A 1 45 ALA 45 112 112 ALA ALA A . n A 1 46 ASN 46 113 113 ASN ASN A . n A 1 47 TYR 47 114 114 TYR TYR A . n A 1 48 LEU 48 115 115 LEU LEU A . n A 1 49 LEU 49 116 116 LEU LEU A . n A 1 50 LYS 50 117 117 LYS LYS A . n A 1 51 ASN 51 118 118 ASN ASN A . n A 1 52 GLY 52 119 119 GLY GLY A . n A 1 53 GLU 53 120 120 GLU GLU A . n A 1 54 THR 54 121 121 THR THR A . n A 1 55 PHE 55 122 122 PHE PHE A . n A 1 56 LEU 56 123 123 LEU LEU A . n A 1 57 LYS 57 124 124 LYS LYS A . n A 1 58 PRO 58 125 125 PRO PRO A . n A 1 59 GLU 59 126 126 GLU GLU A . n A 1 60 ASP 60 127 127 ASP ASP A . n A 1 61 PHE 61 128 128 PHE PHE A . n A 1 62 ASN 62 129 129 ASN ASN A . n A 1 63 PHE 63 130 130 PHE PHE A . n A 1 64 THR 64 131 131 THR THR A . n A 1 65 VAL 65 132 132 VAL VAL A . n A 1 66 LEU 66 133 133 LEU LEU A . n A 1 67 PRO 67 134 134 PRO PRO A . n A 1 68 LYS 68 135 ? ? ? A . n A 1 69 GLY 69 136 ? ? ? A . n B 2 1 DG 1 1 1 DG DG B . n B 2 2 DT 2 2 2 DT DT B . n B 2 3 DC 3 3 3 DC DC B . n B 2 4 DA 4 4 4 DA DA B . n B 2 5 DC 5 5 5 DC DC B . n B 2 6 DT 6 6 6 DT DT B . n B 2 7 DA 7 7 7 DA DA B . n B 2 8 DC 8 8 8 DC DC B . n B 2 9 5CM 9 9 9 5CM 5CM B . n B 2 10 DG 10 10 10 DG DG B . n B 2 11 DG 11 11 11 DG DG B . n B 2 12 DA 12 12 12 DA DA B . n B 2 13 DC 13 13 13 DC DC B . n B 2 14 DA 14 14 14 DA DA B . n C 3 1 DG 1 1 1 DG DG C . n C 3 2 DT 2 2 2 DT DT C . n C 3 3 DC 3 3 3 DC DC C . n C 3 4 5HC 4 4 4 5HC 5HM C . n C 3 5 DG 5 5 5 DG DG C . n C 3 6 DG 6 6 6 DG DG C . n C 3 7 DT 7 7 7 DT DT C . n C 3 8 DA 8 8 8 DA DA C . n C 3 9 DG 9 9 9 DG DG C . n C 3 10 DT 10 10 10 DT DT C . n C 3 11 DG 11 11 11 DG DG C . n C 3 12 DA 12 12 12 DA DA C . n C 3 13 DC 13 13 13 DC DC C . n C 3 14 DT 14 14 14 DT DT C . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code D 4 ACT 1 201 1 ACT ACT A . E 5 EDO 1 202 10 EDO EDO A . F 6 HOH 1 301 2 HOH HOH A . F 6 HOH 2 302 5 HOH HOH A . F 6 HOH 3 303 8 HOH HOH A . F 6 HOH 4 304 11 HOH HOH A . F 6 HOH 5 305 14 HOH HOH A . F 6 HOH 6 306 16 HOH HOH A . F 6 HOH 7 307 19 HOH HOH A . F 6 HOH 8 308 21 HOH HOH A . F 6 HOH 9 309 22 HOH HOH A . F 6 HOH 10 310 25 HOH HOH A . F 6 HOH 11 311 26 HOH HOH A . F 6 HOH 12 312 30 HOH HOH A . F 6 HOH 13 313 31 HOH HOH A . F 6 HOH 14 314 32 HOH HOH A . F 6 HOH 15 315 36 HOH HOH A . F 6 HOH 16 316 40 HOH HOH A . F 6 HOH 17 317 42 HOH HOH A . F 6 HOH 18 318 43 HOH HOH A . F 6 HOH 19 319 45 HOH HOH A . F 6 HOH 20 320 46 HOH HOH A . F 6 HOH 21 321 47 HOH HOH A . F 6 HOH 22 322 48 HOH HOH A . F 6 HOH 23 323 51 HOH HOH A . F 6 HOH 24 324 52 HOH HOH A . F 6 HOH 25 325 55 HOH HOH A . F 6 HOH 26 326 58 HOH HOH A . F 6 HOH 27 327 66 HOH HOH A . F 6 HOH 28 328 67 HOH HOH A . F 6 HOH 29 329 68 HOH HOH A . F 6 HOH 30 330 69 HOH HOH A . F 6 HOH 31 331 71 HOH HOH A . F 6 HOH 32 332 13 HOH HOH A . G 6 HOH 1 101 9 HOH HOH B . G 6 HOH 2 102 10 HOH HOH B . G 6 HOH 3 103 12 HOH HOH B . G 6 HOH 4 104 17 HOH HOH B . G 6 HOH 5 105 23 HOH HOH B . G 6 HOH 6 106 24 HOH HOH B . G 6 HOH 7 107 27 HOH HOH B . G 6 HOH 8 108 28 HOH HOH B . G 6 HOH 9 109 29 HOH HOH B . G 6 HOH 10 110 35 HOH HOH B . G 6 HOH 11 111 41 HOH HOH B . G 6 HOH 12 112 50 HOH HOH B . G 6 HOH 13 113 56 HOH HOH B . G 6 HOH 14 114 59 HOH HOH B . G 6 HOH 15 115 60 HOH HOH B . G 6 HOH 16 116 61 HOH HOH B . G 6 HOH 17 117 62 HOH HOH B . G 6 HOH 18 118 63 HOH HOH B . G 6 HOH 19 119 64 HOH HOH B . H 6 HOH 1 101 39 HOH HOH C . H 6 HOH 2 102 1 HOH HOH C . H 6 HOH 3 103 3 HOH HOH C . H 6 HOH 4 104 4 HOH HOH C . H 6 HOH 5 105 6 HOH HOH C . H 6 HOH 6 106 7 HOH HOH C . H 6 HOH 7 107 15 HOH HOH C . H 6 HOH 8 108 18 HOH HOH C . H 6 HOH 9 109 20 HOH HOH C . H 6 HOH 10 110 33 HOH HOH C . H 6 HOH 11 111 34 HOH HOH C . H 6 HOH 12 112 37 HOH HOH C . H 6 HOH 13 113 38 HOH HOH C . H 6 HOH 14 114 44 HOH HOH C . H 6 HOH 15 115 49 HOH HOH C . H 6 HOH 16 116 53 HOH HOH C . H 6 HOH 17 117 54 HOH HOH C . H 6 HOH 18 118 57 HOH HOH C . H 6 HOH 19 119 65 HOH HOH C . H 6 HOH 20 120 70 HOH HOH C . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 B 5CM 9 B 5CM 9 ? DC ? 2 C 5HC 4 C 5HC 4 ? DC ? # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 3250 ? 1 MORE -8 ? 1 'SSA (A^2)' 10580 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id B _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 101 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id G _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2013-01-16 2 'Structure model' 1 1 2013-08-14 3 'Structure model' 1 2 2023-11-08 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_initial_refinement_model 5 3 'Structure model' struct_conn 6 3 'Structure model' struct_ref_seq_dif 7 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 3 'Structure model' '_struct_ref_seq_dif.details' 5 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 6 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 7 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined 3.7555 12.0077 4.2199 0.1781 0.2414 0.2715 -0.0150 0.0346 0.0650 0.5204 0.7592 0.8684 -0.0042 0.5374 0.1364 -0.0335 0.0180 0.1899 -0.1543 0.1438 0.0997 0.0208 0.0187 -0.1022 'X-RAY DIFFRACTION' 2 ? refined 18.9074 12.4405 -14.1120 0.3464 0.3574 0.5079 -0.1182 0.0550 0.1039 2.3511 0.6930 0.6149 1.1076 0.2227 0.0412 -0.0025 -0.4850 -0.5973 -0.2576 -0.0716 -0.4990 -0.1390 -0.1881 0.0227 'X-RAY DIFFRACTION' 3 ? refined 22.4674 13.8384 -11.5003 0.2686 0.5933 0.3734 -0.0809 0.0508 -0.0093 1.9438 0.4368 0.0450 -0.9158 0.2530 -0.2555 -0.3740 -0.2072 0.4443 -0.2628 0.2009 -0.3107 0.0173 0.1768 0.1312 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection 'X-RAY DIFFRACTION' 1 1 A 72 A 134 'chain A' ? ? ? ? ? 'X-RAY DIFFRACTION' 2 2 B 1 B 14 'chain B' ? ? ? ? ? 'X-RAY DIFFRACTION' 3 3 C 1 C 14 'chain C' ? ? ? ? ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal HKL-2000 'data collection' . ? 1 MOLREP phasing . ? 2 PHENIX refinement '(phenix.refine: 1.6.4_486)' ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "O4'" _pdbx_validate_rmsd_angle.auth_asym_id_1 B _pdbx_validate_rmsd_angle.auth_comp_id_1 DG _pdbx_validate_rmsd_angle.auth_seq_id_1 11 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 "C1'" _pdbx_validate_rmsd_angle.auth_asym_id_2 B _pdbx_validate_rmsd_angle.auth_comp_id_2 DG _pdbx_validate_rmsd_angle.auth_seq_id_2 11 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 N9 _pdbx_validate_rmsd_angle.auth_asym_id_3 B _pdbx_validate_rmsd_angle.auth_comp_id_3 DG _pdbx_validate_rmsd_angle.auth_seq_id_3 11 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 112.96 _pdbx_validate_rmsd_angle.angle_target_value 108.30 _pdbx_validate_rmsd_angle.angle_deviation 4.66 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.30 _pdbx_validate_rmsd_angle.linker_flag N # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A SER 68 ? A SER 1 2 1 Y 1 A GLY 69 ? A GLY 2 3 1 Y 1 A HIS 70 ? A HIS 3 4 1 Y 1 A LYS 71 ? A LYS 4 5 1 Y 1 A LYS 135 ? A LYS 68 6 1 Y 1 A GLY 136 ? A GLY 69 # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal 5CM N1 N N N 1 5CM C2 C N N 2 5CM N3 N N N 3 5CM C4 C N N 4 5CM C5 C N N 5 5CM C5A C N N 6 5CM C6 C N N 7 5CM O2 O N N 8 5CM N4 N N N 9 5CM "C1'" C N R 10 5CM "C2'" C N N 11 5CM "C3'" C N S 12 5CM "C4'" C N R 13 5CM "O4'" O N N 14 5CM "O3'" O N N 15 5CM "C5'" C N N 16 5CM "O5'" O N N 17 5CM P P N N 18 5CM OP1 O N N 19 5CM OP2 O N N 20 5CM OP3 O N N 21 5CM H5A1 H N N 22 5CM H5A2 H N N 23 5CM H5A3 H N N 24 5CM H6 H N N 25 5CM HN41 H N N 26 5CM HN42 H N N 27 5CM "H1'" H N N 28 5CM "H2'" H N N 29 5CM "H2''" H N N 30 5CM "H3'" H N N 31 5CM "H4'" H N N 32 5CM "HO3'" H N N 33 5CM "H5'" H N N 34 5CM "H5''" H N N 35 5CM HOP2 H N N 36 5CM HOP3 H N N 37 5HC P P N N 38 5HC OP1 O N N 39 5HC OP2 O N N 40 5HC "O5'" O N N 41 5HC "C5'" C N N 42 5HC "C4'" C N R 43 5HC "O4'" O N N 44 5HC "C3'" C N S 45 5HC "O3'" O N N 46 5HC "C2'" C N N 47 5HC "C1'" C N R 48 5HC N1 N N N 49 5HC C2 C N N 50 5HC O2 O N N 51 5HC N3 N N N 52 5HC C4 C N N 53 5HC N4 N N N 54 5HC C5 C N N 55 5HC C5M C N N 56 5HC O5 O N N 57 5HC C6 C N N 58 5HC OP3 O N N 59 5HC HOP2 H N N 60 5HC "H5'" H N N 61 5HC "H5''" H N N 62 5HC H4 H N N 63 5HC "H3'" H N N 64 5HC "HO3'" H N N 65 5HC "H2'" H N N 66 5HC "H2''" H N N 67 5HC "H1'" H N N 68 5HC HN41 H N N 69 5HC HN42 H N N 70 5HC H5M2 H N N 71 5HC H5M1 H N N 72 5HC HO5 H N N 73 5HC H6 H N N 74 5HC HOP3 H N N 75 ACT C C N N 76 ACT O O N N 77 ACT OXT O N N 78 ACT CH3 C N N 79 ACT H1 H N N 80 ACT H2 H N N 81 ACT H3 H N N 82 ALA N N N N 83 ALA CA C N S 84 ALA C C N N 85 ALA O O N N 86 ALA CB C N N 87 ALA OXT O N N 88 ALA H H N N 89 ALA H2 H N N 90 ALA HA H N N 91 ALA HB1 H N N 92 ALA HB2 H N N 93 ALA HB3 H N N 94 ALA HXT H N N 95 ARG N N N N 96 ARG CA C N S 97 ARG C C N N 98 ARG O O N N 99 ARG CB C N N 100 ARG CG C N N 101 ARG CD C N N 102 ARG NE N N N 103 ARG CZ C N N 104 ARG NH1 N N N 105 ARG NH2 N N N 106 ARG OXT O N N 107 ARG H H N N 108 ARG H2 H N N 109 ARG HA H N N 110 ARG HB2 H N N 111 ARG HB3 H N N 112 ARG HG2 H N N 113 ARG HG3 H N N 114 ARG HD2 H N N 115 ARG HD3 H N N 116 ARG HE H N N 117 ARG HH11 H N N 118 ARG HH12 H N N 119 ARG HH21 H N N 120 ARG HH22 H N N 121 ARG HXT H N N 122 ASN N N N N 123 ASN CA C N S 124 ASN C C N N 125 ASN O O N N 126 ASN CB C N N 127 ASN CG C N N 128 ASN OD1 O N N 129 ASN ND2 N N N 130 ASN OXT O N N 131 ASN H H N N 132 ASN H2 H N N 133 ASN HA H N N 134 ASN HB2 H N N 135 ASN HB3 H N N 136 ASN HD21 H N N 137 ASN HD22 H N N 138 ASN HXT H N N 139 ASP N N N N 140 ASP CA C N S 141 ASP C C N N 142 ASP O O N N 143 ASP CB C N N 144 ASP CG C N N 145 ASP OD1 O N N 146 ASP OD2 O N N 147 ASP OXT O N N 148 ASP H H N N 149 ASP H2 H N N 150 ASP HA H N N 151 ASP HB2 H N N 152 ASP HB3 H N N 153 ASP HD2 H N N 154 ASP HXT H N N 155 CYS N N N N 156 CYS CA C N R 157 CYS C C N N 158 CYS O O N N 159 CYS CB C N N 160 CYS SG S N N 161 CYS OXT O N N 162 CYS H H N N 163 CYS H2 H N N 164 CYS HA H N N 165 CYS HB2 H N N 166 CYS HB3 H N N 167 CYS HG H N N 168 CYS HXT H N N 169 DA OP3 O N N 170 DA P P N N 171 DA OP1 O N N 172 DA OP2 O N N 173 DA "O5'" O N N 174 DA "C5'" C N N 175 DA "C4'" C N R 176 DA "O4'" O N N 177 DA "C3'" C N S 178 DA "O3'" O N N 179 DA "C2'" C N N 180 DA "C1'" C N R 181 DA N9 N Y N 182 DA C8 C Y N 183 DA N7 N Y N 184 DA C5 C Y N 185 DA C6 C Y N 186 DA N6 N N N 187 DA N1 N Y N 188 DA C2 C Y N 189 DA N3 N Y N 190 DA C4 C Y N 191 DA HOP3 H N N 192 DA HOP2 H N N 193 DA "H5'" H N N 194 DA "H5''" H N N 195 DA "H4'" H N N 196 DA "H3'" H N N 197 DA "HO3'" H N N 198 DA "H2'" H N N 199 DA "H2''" H N N 200 DA "H1'" H N N 201 DA H8 H N N 202 DA H61 H N N 203 DA H62 H N N 204 DA H2 H N N 205 DC OP3 O N N 206 DC P P N N 207 DC OP1 O N N 208 DC OP2 O N N 209 DC "O5'" O N N 210 DC "C5'" C N N 211 DC "C4'" C N R 212 DC "O4'" O N N 213 DC "C3'" C N S 214 DC "O3'" O N N 215 DC "C2'" C N N 216 DC "C1'" C N R 217 DC N1 N N N 218 DC C2 C N N 219 DC O2 O N N 220 DC N3 N N N 221 DC C4 C N N 222 DC N4 N N N 223 DC C5 C N N 224 DC C6 C N N 225 DC HOP3 H N N 226 DC HOP2 H N N 227 DC "H5'" H N N 228 DC "H5''" H N N 229 DC "H4'" H N N 230 DC "H3'" H N N 231 DC "HO3'" H N N 232 DC "H2'" H N N 233 DC "H2''" H N N 234 DC "H1'" H N N 235 DC H41 H N N 236 DC H42 H N N 237 DC H5 H N N 238 DC H6 H N N 239 DG OP3 O N N 240 DG P P N N 241 DG OP1 O N N 242 DG OP2 O N N 243 DG "O5'" O N N 244 DG "C5'" C N N 245 DG "C4'" C N R 246 DG "O4'" O N N 247 DG "C3'" C N S 248 DG "O3'" O N N 249 DG "C2'" C N N 250 DG "C1'" C N R 251 DG N9 N Y N 252 DG C8 C Y N 253 DG N7 N Y N 254 DG C5 C Y N 255 DG C6 C N N 256 DG O6 O N N 257 DG N1 N N N 258 DG C2 C N N 259 DG N2 N N N 260 DG N3 N N N 261 DG C4 C Y N 262 DG HOP3 H N N 263 DG HOP2 H N N 264 DG "H5'" H N N 265 DG "H5''" H N N 266 DG "H4'" H N N 267 DG "H3'" H N N 268 DG "HO3'" H N N 269 DG "H2'" H N N 270 DG "H2''" H N N 271 DG "H1'" H N N 272 DG H8 H N N 273 DG H1 H N N 274 DG H21 H N N 275 DG H22 H N N 276 DT OP3 O N N 277 DT P P N N 278 DT OP1 O N N 279 DT OP2 O N N 280 DT "O5'" O N N 281 DT "C5'" C N N 282 DT "C4'" C N R 283 DT "O4'" O N N 284 DT "C3'" C N S 285 DT "O3'" O N N 286 DT "C2'" C N N 287 DT "C1'" C N R 288 DT N1 N N N 289 DT C2 C N N 290 DT O2 O N N 291 DT N3 N N N 292 DT C4 C N N 293 DT O4 O N N 294 DT C5 C N N 295 DT C7 C N N 296 DT C6 C N N 297 DT HOP3 H N N 298 DT HOP2 H N N 299 DT "H5'" H N N 300 DT "H5''" H N N 301 DT "H4'" H N N 302 DT "H3'" H N N 303 DT "HO3'" H N N 304 DT "H2'" H N N 305 DT "H2''" H N N 306 DT "H1'" H N N 307 DT H3 H N N 308 DT H71 H N N 309 DT H72 H N N 310 DT H73 H N N 311 DT H6 H N N 312 EDO C1 C N N 313 EDO O1 O N N 314 EDO C2 C N N 315 EDO O2 O N N 316 EDO H11 H N N 317 EDO H12 H N N 318 EDO HO1 H N N 319 EDO H21 H N N 320 EDO H22 H N N 321 EDO HO2 H N N 322 GLN N N N N 323 GLN CA C N S 324 GLN C C N N 325 GLN O O N N 326 GLN CB C N N 327 GLN CG C N N 328 GLN CD C N N 329 GLN OE1 O N N 330 GLN NE2 N N N 331 GLN OXT O N N 332 GLN H H N N 333 GLN H2 H N N 334 GLN HA H N N 335 GLN HB2 H N N 336 GLN HB3 H N N 337 GLN HG2 H N N 338 GLN HG3 H N N 339 GLN HE21 H N N 340 GLN HE22 H N N 341 GLN HXT H N N 342 GLU N N N N 343 GLU CA C N S 344 GLU C C N N 345 GLU O O N N 346 GLU CB C N N 347 GLU CG C N N 348 GLU CD C N N 349 GLU OE1 O N N 350 GLU OE2 O N N 351 GLU OXT O N N 352 GLU H H N N 353 GLU H2 H N N 354 GLU HA H N N 355 GLU HB2 H N N 356 GLU HB3 H N N 357 GLU HG2 H N N 358 GLU HG3 H N N 359 GLU HE2 H N N 360 GLU HXT H N N 361 GLY N N N N 362 GLY CA C N N 363 GLY C C N N 364 GLY O O N N 365 GLY OXT O N N 366 GLY H H N N 367 GLY H2 H N N 368 GLY HA2 H N N 369 GLY HA3 H N N 370 GLY HXT H N N 371 HIS N N N N 372 HIS CA C N S 373 HIS C C N N 374 HIS O O N N 375 HIS CB C N N 376 HIS CG C Y N 377 HIS ND1 N Y N 378 HIS CD2 C Y N 379 HIS CE1 C Y N 380 HIS NE2 N Y N 381 HIS OXT O N N 382 HIS H H N N 383 HIS H2 H N N 384 HIS HA H N N 385 HIS HB2 H N N 386 HIS HB3 H N N 387 HIS HD1 H N N 388 HIS HD2 H N N 389 HIS HE1 H N N 390 HIS HE2 H N N 391 HIS HXT H N N 392 HOH O O N N 393 HOH H1 H N N 394 HOH H2 H N N 395 ILE N N N N 396 ILE CA C N S 397 ILE C C N N 398 ILE O O N N 399 ILE CB C N S 400 ILE CG1 C N N 401 ILE CG2 C N N 402 ILE CD1 C N N 403 ILE OXT O N N 404 ILE H H N N 405 ILE H2 H N N 406 ILE HA H N N 407 ILE HB H N N 408 ILE HG12 H N N 409 ILE HG13 H N N 410 ILE HG21 H N N 411 ILE HG22 H N N 412 ILE HG23 H N N 413 ILE HD11 H N N 414 ILE HD12 H N N 415 ILE HD13 H N N 416 ILE HXT H N N 417 LEU N N N N 418 LEU CA C N S 419 LEU C C N N 420 LEU O O N N 421 LEU CB C N N 422 LEU CG C N N 423 LEU CD1 C N N 424 LEU CD2 C N N 425 LEU OXT O N N 426 LEU H H N N 427 LEU H2 H N N 428 LEU HA H N N 429 LEU HB2 H N N 430 LEU HB3 H N N 431 LEU HG H N N 432 LEU HD11 H N N 433 LEU HD12 H N N 434 LEU HD13 H N N 435 LEU HD21 H N N 436 LEU HD22 H N N 437 LEU HD23 H N N 438 LEU HXT H N N 439 LYS N N N N 440 LYS CA C N S 441 LYS C C N N 442 LYS O O N N 443 LYS CB C N N 444 LYS CG C N N 445 LYS CD C N N 446 LYS CE C N N 447 LYS NZ N N N 448 LYS OXT O N N 449 LYS H H N N 450 LYS H2 H N N 451 LYS HA H N N 452 LYS HB2 H N N 453 LYS HB3 H N N 454 LYS HG2 H N N 455 LYS HG3 H N N 456 LYS HD2 H N N 457 LYS HD3 H N N 458 LYS HE2 H N N 459 LYS HE3 H N N 460 LYS HZ1 H N N 461 LYS HZ2 H N N 462 LYS HZ3 H N N 463 LYS HXT H N N 464 PHE N N N N 465 PHE CA C N S 466 PHE C C N N 467 PHE O O N N 468 PHE CB C N N 469 PHE CG C Y N 470 PHE CD1 C Y N 471 PHE CD2 C Y N 472 PHE CE1 C Y N 473 PHE CE2 C Y N 474 PHE CZ C Y N 475 PHE OXT O N N 476 PHE H H N N 477 PHE H2 H N N 478 PHE HA H N N 479 PHE HB2 H N N 480 PHE HB3 H N N 481 PHE HD1 H N N 482 PHE HD2 H N N 483 PHE HE1 H N N 484 PHE HE2 H N N 485 PHE HZ H N N 486 PHE HXT H N N 487 PRO N N N N 488 PRO CA C N S 489 PRO C C N N 490 PRO O O N N 491 PRO CB C N N 492 PRO CG C N N 493 PRO CD C N N 494 PRO OXT O N N 495 PRO H H N N 496 PRO HA H N N 497 PRO HB2 H N N 498 PRO HB3 H N N 499 PRO HG2 H N N 500 PRO HG3 H N N 501 PRO HD2 H N N 502 PRO HD3 H N N 503 PRO HXT H N N 504 SER N N N N 505 SER CA C N S 506 SER C C N N 507 SER O O N N 508 SER CB C N N 509 SER OG O N N 510 SER OXT O N N 511 SER H H N N 512 SER H2 H N N 513 SER HA H N N 514 SER HB2 H N N 515 SER HB3 H N N 516 SER HG H N N 517 SER HXT H N N 518 THR N N N N 519 THR CA C N S 520 THR C C N N 521 THR O O N N 522 THR CB C N R 523 THR OG1 O N N 524 THR CG2 C N N 525 THR OXT O N N 526 THR H H N N 527 THR H2 H N N 528 THR HA H N N 529 THR HB H N N 530 THR HG1 H N N 531 THR HG21 H N N 532 THR HG22 H N N 533 THR HG23 H N N 534 THR HXT H N N 535 TRP N N N N 536 TRP CA C N S 537 TRP C C N N 538 TRP O O N N 539 TRP CB C N N 540 TRP CG C Y N 541 TRP CD1 C Y N 542 TRP CD2 C Y N 543 TRP NE1 N Y N 544 TRP CE2 C Y N 545 TRP CE3 C Y N 546 TRP CZ2 C Y N 547 TRP CZ3 C Y N 548 TRP CH2 C Y N 549 TRP OXT O N N 550 TRP H H N N 551 TRP H2 H N N 552 TRP HA H N N 553 TRP HB2 H N N 554 TRP HB3 H N N 555 TRP HD1 H N N 556 TRP HE1 H N N 557 TRP HE3 H N N 558 TRP HZ2 H N N 559 TRP HZ3 H N N 560 TRP HH2 H N N 561 TRP HXT H N N 562 TYR N N N N 563 TYR CA C N S 564 TYR C C N N 565 TYR O O N N 566 TYR CB C N N 567 TYR CG C Y N 568 TYR CD1 C Y N 569 TYR CD2 C Y N 570 TYR CE1 C Y N 571 TYR CE2 C Y N 572 TYR CZ C Y N 573 TYR OH O N N 574 TYR OXT O N N 575 TYR H H N N 576 TYR H2 H N N 577 TYR HA H N N 578 TYR HB2 H N N 579 TYR HB3 H N N 580 TYR HD1 H N N 581 TYR HD2 H N N 582 TYR HE1 H N N 583 TYR HE2 H N N 584 TYR HH H N N 585 TYR HXT H N N 586 VAL N N N N 587 VAL CA C N S 588 VAL C C N N 589 VAL O O N N 590 VAL CB C N N 591 VAL CG1 C N N 592 VAL CG2 C N N 593 VAL OXT O N N 594 VAL H H N N 595 VAL H2 H N N 596 VAL HA H N N 597 VAL HB H N N 598 VAL HG11 H N N 599 VAL HG12 H N N 600 VAL HG13 H N N 601 VAL HG21 H N N 602 VAL HG22 H N N 603 VAL HG23 H N N 604 VAL HXT H N N 605 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal 5CM N1 C2 sing N N 1 5CM N1 C6 sing N N 2 5CM N1 "C1'" sing N N 3 5CM C2 N3 sing N N 4 5CM C2 O2 doub N N 5 5CM N3 C4 doub N N 6 5CM C4 C5 sing N N 7 5CM C4 N4 sing N N 8 5CM C5 C5A sing N N 9 5CM C5 C6 doub N N 10 5CM C5A H5A1 sing N N 11 5CM C5A H5A2 sing N N 12 5CM C5A H5A3 sing N N 13 5CM C6 H6 sing N N 14 5CM N4 HN41 sing N N 15 5CM N4 HN42 sing N N 16 5CM "C1'" "C2'" sing N N 17 5CM "C1'" "O4'" sing N N 18 5CM "C1'" "H1'" sing N N 19 5CM "C2'" "C3'" sing N N 20 5CM "C2'" "H2'" sing N N 21 5CM "C2'" "H2''" sing N N 22 5CM "C3'" "C4'" sing N N 23 5CM "C3'" "O3'" sing N N 24 5CM "C3'" "H3'" sing N N 25 5CM "C4'" "O4'" sing N N 26 5CM "C4'" "C5'" sing N N 27 5CM "C4'" "H4'" sing N N 28 5CM "O3'" "HO3'" sing N N 29 5CM "C5'" "O5'" sing N N 30 5CM "C5'" "H5'" sing N N 31 5CM "C5'" "H5''" sing N N 32 5CM "O5'" P sing N N 33 5CM P OP1 doub N N 34 5CM P OP2 sing N N 35 5CM P OP3 sing N N 36 5CM OP2 HOP2 sing N N 37 5CM OP3 HOP3 sing N N 38 5HC "O4'" "C4'" sing N N 39 5HC "O4'" "C1'" sing N N 40 5HC "C4'" "C5'" sing N N 41 5HC "C4'" "C3'" sing N N 42 5HC O2 C2 doub N N 43 5HC "C1'" N1 sing N N 44 5HC "C1'" "C2'" sing N N 45 5HC "C5'" "O5'" sing N N 46 5HC C2 N1 sing N N 47 5HC C2 N3 sing N N 48 5HC N1 C6 sing N N 49 5HC N3 C4 doub N N 50 5HC "O5'" P sing N N 51 5HC "C2'" "C3'" sing N N 52 5HC C6 C5 doub N N 53 5HC "C3'" "O3'" sing N N 54 5HC P OP1 doub N N 55 5HC P OP2 sing N N 56 5HC C4 C5 sing N N 57 5HC C4 N4 sing N N 58 5HC C5 C5M sing N N 59 5HC C5M O5 sing N N 60 5HC P OP3 sing N N 61 5HC OP2 HOP2 sing N N 62 5HC "C5'" "H5'" sing N N 63 5HC "C5'" "H5''" sing N N 64 5HC "C4'" H4 sing N N 65 5HC "C3'" "H3'" sing N N 66 5HC "O3'" "HO3'" sing N N 67 5HC "C2'" "H2'" sing N N 68 5HC "C2'" "H2''" sing N N 69 5HC "C1'" "H1'" sing N N 70 5HC N4 HN41 sing N N 71 5HC N4 HN42 sing N N 72 5HC C5M H5M2 sing N N 73 5HC C5M H5M1 sing N N 74 5HC O5 HO5 sing N N 75 5HC C6 H6 sing N N 76 5HC OP3 HOP3 sing N N 77 ACT C O doub N N 78 ACT C OXT sing N N 79 ACT C CH3 sing N N 80 ACT CH3 H1 sing N N 81 ACT CH3 H2 sing N N 82 ACT CH3 H3 sing N N 83 ALA N CA sing N N 84 ALA N H sing N N 85 ALA N H2 sing N N 86 ALA CA C sing N N 87 ALA CA CB sing N N 88 ALA CA HA sing N N 89 ALA C O doub N N 90 ALA C OXT sing N N 91 ALA CB HB1 sing N N 92 ALA CB HB2 sing N N 93 ALA CB HB3 sing N N 94 ALA OXT HXT sing N N 95 ARG N CA sing N N 96 ARG N H sing N N 97 ARG N H2 sing N N 98 ARG CA C sing N N 99 ARG CA CB sing N N 100 ARG CA HA sing N N 101 ARG C O doub N N 102 ARG C OXT sing N N 103 ARG CB CG sing N N 104 ARG CB HB2 sing N N 105 ARG CB HB3 sing N N 106 ARG CG CD sing N N 107 ARG CG HG2 sing N N 108 ARG CG HG3 sing N N 109 ARG CD NE sing N N 110 ARG CD HD2 sing N N 111 ARG CD HD3 sing N N 112 ARG NE CZ sing N N 113 ARG NE HE sing N N 114 ARG CZ NH1 sing N N 115 ARG CZ NH2 doub N N 116 ARG NH1 HH11 sing N N 117 ARG NH1 HH12 sing N N 118 ARG NH2 HH21 sing N N 119 ARG NH2 HH22 sing N N 120 ARG OXT HXT sing N N 121 ASN N CA sing N N 122 ASN N H sing N N 123 ASN N H2 sing N N 124 ASN CA C sing N N 125 ASN CA CB sing N N 126 ASN CA HA sing N N 127 ASN C O doub N N 128 ASN C OXT sing N N 129 ASN CB CG sing N N 130 ASN CB HB2 sing N N 131 ASN CB HB3 sing N N 132 ASN CG OD1 doub N N 133 ASN CG ND2 sing N N 134 ASN ND2 HD21 sing N N 135 ASN ND2 HD22 sing N N 136 ASN OXT HXT sing N N 137 ASP N CA sing N N 138 ASP N H sing N N 139 ASP N H2 sing N N 140 ASP CA C sing N N 141 ASP CA CB sing N N 142 ASP CA HA sing N N 143 ASP C O doub N N 144 ASP C OXT sing N N 145 ASP CB CG sing N N 146 ASP CB HB2 sing N N 147 ASP CB HB3 sing N N 148 ASP CG OD1 doub N N 149 ASP CG OD2 sing N N 150 ASP OD2 HD2 sing N N 151 ASP OXT HXT sing N N 152 CYS N CA sing N N 153 CYS N H sing N N 154 CYS N H2 sing N N 155 CYS CA C sing N N 156 CYS CA CB sing N N 157 CYS CA HA sing N N 158 CYS C O doub N N 159 CYS C OXT sing N N 160 CYS CB SG sing N N 161 CYS CB HB2 sing N N 162 CYS CB HB3 sing N N 163 CYS SG HG sing N N 164 CYS OXT HXT sing N N 165 DA OP3 P sing N N 166 DA OP3 HOP3 sing N N 167 DA P OP1 doub N N 168 DA P OP2 sing N N 169 DA P "O5'" sing N N 170 DA OP2 HOP2 sing N N 171 DA "O5'" "C5'" sing N N 172 DA "C5'" "C4'" sing N N 173 DA "C5'" "H5'" sing N N 174 DA "C5'" "H5''" sing N N 175 DA "C4'" "O4'" sing N N 176 DA "C4'" "C3'" sing N N 177 DA "C4'" "H4'" sing N N 178 DA "O4'" "C1'" sing N N 179 DA "C3'" "O3'" sing N N 180 DA "C3'" "C2'" sing N N 181 DA "C3'" "H3'" sing N N 182 DA "O3'" "HO3'" sing N N 183 DA "C2'" "C1'" sing N N 184 DA "C2'" "H2'" sing N N 185 DA "C2'" "H2''" sing N N 186 DA "C1'" N9 sing N N 187 DA "C1'" "H1'" sing N N 188 DA N9 C8 sing Y N 189 DA N9 C4 sing Y N 190 DA C8 N7 doub Y N 191 DA C8 H8 sing N N 192 DA N7 C5 sing Y N 193 DA C5 C6 sing Y N 194 DA C5 C4 doub Y N 195 DA C6 N6 sing N N 196 DA C6 N1 doub Y N 197 DA N6 H61 sing N N 198 DA N6 H62 sing N N 199 DA N1 C2 sing Y N 200 DA C2 N3 doub Y N 201 DA C2 H2 sing N N 202 DA N3 C4 sing Y N 203 DC OP3 P sing N N 204 DC OP3 HOP3 sing N N 205 DC P OP1 doub N N 206 DC P OP2 sing N N 207 DC P "O5'" sing N N 208 DC OP2 HOP2 sing N N 209 DC "O5'" "C5'" sing N N 210 DC "C5'" "C4'" sing N N 211 DC "C5'" "H5'" sing N N 212 DC "C5'" "H5''" sing N N 213 DC "C4'" "O4'" sing N N 214 DC "C4'" "C3'" sing N N 215 DC "C4'" "H4'" sing N N 216 DC "O4'" "C1'" sing N N 217 DC "C3'" "O3'" sing N N 218 DC "C3'" "C2'" sing N N 219 DC "C3'" "H3'" sing N N 220 DC "O3'" "HO3'" sing N N 221 DC "C2'" "C1'" sing N N 222 DC "C2'" "H2'" sing N N 223 DC "C2'" "H2''" sing N N 224 DC "C1'" N1 sing N N 225 DC "C1'" "H1'" sing N N 226 DC N1 C2 sing N N 227 DC N1 C6 sing N N 228 DC C2 O2 doub N N 229 DC C2 N3 sing N N 230 DC N3 C4 doub N N 231 DC C4 N4 sing N N 232 DC C4 C5 sing N N 233 DC N4 H41 sing N N 234 DC N4 H42 sing N N 235 DC C5 C6 doub N N 236 DC C5 H5 sing N N 237 DC C6 H6 sing N N 238 DG OP3 P sing N N 239 DG OP3 HOP3 sing N N 240 DG P OP1 doub N N 241 DG P OP2 sing N N 242 DG P "O5'" sing N N 243 DG OP2 HOP2 sing N N 244 DG "O5'" "C5'" sing N N 245 DG "C5'" "C4'" sing N N 246 DG "C5'" "H5'" sing N N 247 DG "C5'" "H5''" sing N N 248 DG "C4'" "O4'" sing N N 249 DG "C4'" "C3'" sing N N 250 DG "C4'" "H4'" sing N N 251 DG "O4'" "C1'" sing N N 252 DG "C3'" "O3'" sing N N 253 DG "C3'" "C2'" sing N N 254 DG "C3'" "H3'" sing N N 255 DG "O3'" "HO3'" sing N N 256 DG "C2'" "C1'" sing N N 257 DG "C2'" "H2'" sing N N 258 DG "C2'" "H2''" sing N N 259 DG "C1'" N9 sing N N 260 DG "C1'" "H1'" sing N N 261 DG N9 C8 sing Y N 262 DG N9 C4 sing Y N 263 DG C8 N7 doub Y N 264 DG C8 H8 sing N N 265 DG N7 C5 sing Y N 266 DG C5 C6 sing N N 267 DG C5 C4 doub Y N 268 DG C6 O6 doub N N 269 DG C6 N1 sing N N 270 DG N1 C2 sing N N 271 DG N1 H1 sing N N 272 DG C2 N2 sing N N 273 DG C2 N3 doub N N 274 DG N2 H21 sing N N 275 DG N2 H22 sing N N 276 DG N3 C4 sing N N 277 DT OP3 P sing N N 278 DT OP3 HOP3 sing N N 279 DT P OP1 doub N N 280 DT P OP2 sing N N 281 DT P "O5'" sing N N 282 DT OP2 HOP2 sing N N 283 DT "O5'" "C5'" sing N N 284 DT "C5'" "C4'" sing N N 285 DT "C5'" "H5'" sing N N 286 DT "C5'" "H5''" sing N N 287 DT "C4'" "O4'" sing N N 288 DT "C4'" "C3'" sing N N 289 DT "C4'" "H4'" sing N N 290 DT "O4'" "C1'" sing N N 291 DT "C3'" "O3'" sing N N 292 DT "C3'" "C2'" sing N N 293 DT "C3'" "H3'" sing N N 294 DT "O3'" "HO3'" sing N N 295 DT "C2'" "C1'" sing N N 296 DT "C2'" "H2'" sing N N 297 DT "C2'" "H2''" sing N N 298 DT "C1'" N1 sing N N 299 DT "C1'" "H1'" sing N N 300 DT N1 C2 sing N N 301 DT N1 C6 sing N N 302 DT C2 O2 doub N N 303 DT C2 N3 sing N N 304 DT N3 C4 sing N N 305 DT N3 H3 sing N N 306 DT C4 O4 doub N N 307 DT C4 C5 sing N N 308 DT C5 C7 sing N N 309 DT C5 C6 doub N N 310 DT C7 H71 sing N N 311 DT C7 H72 sing N N 312 DT C7 H73 sing N N 313 DT C6 H6 sing N N 314 EDO C1 O1 sing N N 315 EDO C1 C2 sing N N 316 EDO C1 H11 sing N N 317 EDO C1 H12 sing N N 318 EDO O1 HO1 sing N N 319 EDO C2 O2 sing N N 320 EDO C2 H21 sing N N 321 EDO C2 H22 sing N N 322 EDO O2 HO2 sing N N 323 GLN N CA sing N N 324 GLN N H sing N N 325 GLN N H2 sing N N 326 GLN CA C sing N N 327 GLN CA CB sing N N 328 GLN CA HA sing N N 329 GLN C O doub N N 330 GLN C OXT sing N N 331 GLN CB CG sing N N 332 GLN CB HB2 sing N N 333 GLN CB HB3 sing N N 334 GLN CG CD sing N N 335 GLN CG HG2 sing N N 336 GLN CG HG3 sing N N 337 GLN CD OE1 doub N N 338 GLN CD NE2 sing N N 339 GLN NE2 HE21 sing N N 340 GLN NE2 HE22 sing N N 341 GLN OXT HXT sing N N 342 GLU N CA sing N N 343 GLU N H sing N N 344 GLU N H2 sing N N 345 GLU CA C sing N N 346 GLU CA CB sing N N 347 GLU CA HA sing N N 348 GLU C O doub N N 349 GLU C OXT sing N N 350 GLU CB CG sing N N 351 GLU CB HB2 sing N N 352 GLU CB HB3 sing N N 353 GLU CG CD sing N N 354 GLU CG HG2 sing N N 355 GLU CG HG3 sing N N 356 GLU CD OE1 doub N N 357 GLU CD OE2 sing N N 358 GLU OE2 HE2 sing N N 359 GLU OXT HXT sing N N 360 GLY N CA sing N N 361 GLY N H sing N N 362 GLY N H2 sing N N 363 GLY CA C sing N N 364 GLY CA HA2 sing N N 365 GLY CA HA3 sing N N 366 GLY C O doub N N 367 GLY C OXT sing N N 368 GLY OXT HXT sing N N 369 HIS N CA sing N N 370 HIS N H sing N N 371 HIS N H2 sing N N 372 HIS CA C sing N N 373 HIS CA CB sing N N 374 HIS CA HA sing N N 375 HIS C O doub N N 376 HIS C OXT sing N N 377 HIS CB CG sing N N 378 HIS CB HB2 sing N N 379 HIS CB HB3 sing N N 380 HIS CG ND1 sing Y N 381 HIS CG CD2 doub Y N 382 HIS ND1 CE1 doub Y N 383 HIS ND1 HD1 sing N N 384 HIS CD2 NE2 sing Y N 385 HIS CD2 HD2 sing N N 386 HIS CE1 NE2 sing Y N 387 HIS CE1 HE1 sing N N 388 HIS NE2 HE2 sing N N 389 HIS OXT HXT sing N N 390 HOH O H1 sing N N 391 HOH O H2 sing N N 392 ILE N CA sing N N 393 ILE N H sing N N 394 ILE N H2 sing N N 395 ILE CA C sing N N 396 ILE CA CB sing N N 397 ILE CA HA sing N N 398 ILE C O doub N N 399 ILE C OXT sing N N 400 ILE CB CG1 sing N N 401 ILE CB CG2 sing N N 402 ILE CB HB sing N N 403 ILE CG1 CD1 sing N N 404 ILE CG1 HG12 sing N N 405 ILE CG1 HG13 sing N N 406 ILE CG2 HG21 sing N N 407 ILE CG2 HG22 sing N N 408 ILE CG2 HG23 sing N N 409 ILE CD1 HD11 sing N N 410 ILE CD1 HD12 sing N N 411 ILE CD1 HD13 sing N N 412 ILE OXT HXT sing N N 413 LEU N CA sing N N 414 LEU N H sing N N 415 LEU N H2 sing N N 416 LEU CA C sing N N 417 LEU CA CB sing N N 418 LEU CA HA sing N N 419 LEU C O doub N N 420 LEU C OXT sing N N 421 LEU CB CG sing N N 422 LEU CB HB2 sing N N 423 LEU CB HB3 sing N N 424 LEU CG CD1 sing N N 425 LEU CG CD2 sing N N 426 LEU CG HG sing N N 427 LEU CD1 HD11 sing N N 428 LEU CD1 HD12 sing N N 429 LEU CD1 HD13 sing N N 430 LEU CD2 HD21 sing N N 431 LEU CD2 HD22 sing N N 432 LEU CD2 HD23 sing N N 433 LEU OXT HXT sing N N 434 LYS N CA sing N N 435 LYS N H sing N N 436 LYS N H2 sing N N 437 LYS CA C sing N N 438 LYS CA CB sing N N 439 LYS CA HA sing N N 440 LYS C O doub N N 441 LYS C OXT sing N N 442 LYS CB CG sing N N 443 LYS CB HB2 sing N N 444 LYS CB HB3 sing N N 445 LYS CG CD sing N N 446 LYS CG HG2 sing N N 447 LYS CG HG3 sing N N 448 LYS CD CE sing N N 449 LYS CD HD2 sing N N 450 LYS CD HD3 sing N N 451 LYS CE NZ sing N N 452 LYS CE HE2 sing N N 453 LYS CE HE3 sing N N 454 LYS NZ HZ1 sing N N 455 LYS NZ HZ2 sing N N 456 LYS NZ HZ3 sing N N 457 LYS OXT HXT sing N N 458 PHE N CA sing N N 459 PHE N H sing N N 460 PHE N H2 sing N N 461 PHE CA C sing N N 462 PHE CA CB sing N N 463 PHE CA HA sing N N 464 PHE C O doub N N 465 PHE C OXT sing N N 466 PHE CB CG sing N N 467 PHE CB HB2 sing N N 468 PHE CB HB3 sing N N 469 PHE CG CD1 doub Y N 470 PHE CG CD2 sing Y N 471 PHE CD1 CE1 sing Y N 472 PHE CD1 HD1 sing N N 473 PHE CD2 CE2 doub Y N 474 PHE CD2 HD2 sing N N 475 PHE CE1 CZ doub Y N 476 PHE CE1 HE1 sing N N 477 PHE CE2 CZ sing Y N 478 PHE CE2 HE2 sing N N 479 PHE CZ HZ sing N N 480 PHE OXT HXT sing N N 481 PRO N CA sing N N 482 PRO N CD sing N N 483 PRO N H sing N N 484 PRO CA C sing N N 485 PRO CA CB sing N N 486 PRO CA HA sing N N 487 PRO C O doub N N 488 PRO C OXT sing N N 489 PRO CB CG sing N N 490 PRO CB HB2 sing N N 491 PRO CB HB3 sing N N 492 PRO CG CD sing N N 493 PRO CG HG2 sing N N 494 PRO CG HG3 sing N N 495 PRO CD HD2 sing N N 496 PRO CD HD3 sing N N 497 PRO OXT HXT sing N N 498 SER N CA sing N N 499 SER N H sing N N 500 SER N H2 sing N N 501 SER CA C sing N N 502 SER CA CB sing N N 503 SER CA HA sing N N 504 SER C O doub N N 505 SER C OXT sing N N 506 SER CB OG sing N N 507 SER CB HB2 sing N N 508 SER CB HB3 sing N N 509 SER OG HG sing N N 510 SER OXT HXT sing N N 511 THR N CA sing N N 512 THR N H sing N N 513 THR N H2 sing N N 514 THR CA C sing N N 515 THR CA CB sing N N 516 THR CA HA sing N N 517 THR C O doub N N 518 THR C OXT sing N N 519 THR CB OG1 sing N N 520 THR CB CG2 sing N N 521 THR CB HB sing N N 522 THR OG1 HG1 sing N N 523 THR CG2 HG21 sing N N 524 THR CG2 HG22 sing N N 525 THR CG2 HG23 sing N N 526 THR OXT HXT sing N N 527 TRP N CA sing N N 528 TRP N H sing N N 529 TRP N H2 sing N N 530 TRP CA C sing N N 531 TRP CA CB sing N N 532 TRP CA HA sing N N 533 TRP C O doub N N 534 TRP C OXT sing N N 535 TRP CB CG sing N N 536 TRP CB HB2 sing N N 537 TRP CB HB3 sing N N 538 TRP CG CD1 doub Y N 539 TRP CG CD2 sing Y N 540 TRP CD1 NE1 sing Y N 541 TRP CD1 HD1 sing N N 542 TRP CD2 CE2 doub Y N 543 TRP CD2 CE3 sing Y N 544 TRP NE1 CE2 sing Y N 545 TRP NE1 HE1 sing N N 546 TRP CE2 CZ2 sing Y N 547 TRP CE3 CZ3 doub Y N 548 TRP CE3 HE3 sing N N 549 TRP CZ2 CH2 doub Y N 550 TRP CZ2 HZ2 sing N N 551 TRP CZ3 CH2 sing Y N 552 TRP CZ3 HZ3 sing N N 553 TRP CH2 HH2 sing N N 554 TRP OXT HXT sing N N 555 TYR N CA sing N N 556 TYR N H sing N N 557 TYR N H2 sing N N 558 TYR CA C sing N N 559 TYR CA CB sing N N 560 TYR CA HA sing N N 561 TYR C O doub N N 562 TYR C OXT sing N N 563 TYR CB CG sing N N 564 TYR CB HB2 sing N N 565 TYR CB HB3 sing N N 566 TYR CG CD1 doub Y N 567 TYR CG CD2 sing Y N 568 TYR CD1 CE1 sing Y N 569 TYR CD1 HD1 sing N N 570 TYR CD2 CE2 doub Y N 571 TYR CD2 HD2 sing N N 572 TYR CE1 CZ doub Y N 573 TYR CE1 HE1 sing N N 574 TYR CE2 CZ sing Y N 575 TYR CE2 HE2 sing N N 576 TYR CZ OH sing N N 577 TYR OH HH sing N N 578 TYR OXT HXT sing N N 579 VAL N CA sing N N 580 VAL N H sing N N 581 VAL N H2 sing N N 582 VAL CA C sing N N 583 VAL CA CB sing N N 584 VAL CA HA sing N N 585 VAL C O doub N N 586 VAL C OXT sing N N 587 VAL CB CG1 sing N N 588 VAL CB CG2 sing N N 589 VAL CB HB sing N N 590 VAL CG1 HG11 sing N N 591 VAL CG1 HG12 sing N N 592 VAL CG1 HG13 sing N N 593 VAL CG2 HG21 sing N N 594 VAL CG2 HG22 sing N N 595 VAL CG2 HG23 sing N N 596 VAL OXT HXT sing N N 597 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3VYB 'double helix' 3VYB 'b-form double helix' 3VYB 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 B DG 1 1_555 C DC 13 1_555 -0.319 0.038 -0.144 -26.739 -17.226 0.231 1 B_DG1:DC13_C B 1 ? C 13 ? 19 1 1 B DT 2 1_555 C DA 12 1_555 -0.503 0.073 -0.011 -10.893 -10.534 -4.546 2 B_DT2:DA12_C B 2 ? C 12 ? 20 1 1 B DC 3 1_555 C DG 11 1_555 -0.013 -0.037 -0.177 -2.889 -3.934 1.502 3 B_DC3:DG11_C B 3 ? C 11 ? 19 1 1 B DA 4 1_555 C DT 10 1_555 0.589 0.115 -0.064 0.282 -12.127 5.729 4 B_DA4:DT10_C B 4 ? C 10 ? 20 1 1 B DC 5 1_555 C DG 9 1_555 0.564 -0.092 0.052 5.967 -17.236 5.404 5 B_DC5:DG9_C B 5 ? C 9 ? 19 1 1 B DT 6 1_555 C DA 8 1_555 -0.282 -0.037 -0.043 -0.578 -13.758 0.891 6 B_DT6:DA8_C B 6 ? C 8 ? 20 1 1 B DA 7 1_555 C DT 7 1_555 0.266 0.014 -0.043 -5.904 -13.062 1.699 7 B_DA7:DT7_C B 7 ? C 7 ? 20 1 1 B DC 8 1_555 C DG 6 1_555 0.441 0.060 0.318 -5.070 -5.702 0.695 8 B_DC8:DG6_C B 8 ? C 6 ? 19 1 1 B 5CM 9 1_555 C DG 5 1_555 0.380 -0.059 -0.169 7.480 -6.857 -1.535 9 B_5CM9:DG5_C B 9 ? C 5 ? 19 1 1 B DG 11 1_555 C DC 3 1_555 -0.221 -0.034 0.286 28.458 4.535 0.983 10 B_DG11:DC3_C B 11 ? C 3 ? 19 1 1 B DA 12 1_555 C DT 2 1_555 -0.041 -0.119 0.442 20.432 -17.314 -0.320 11 B_DA12:DT2_C B 12 ? C 2 ? 20 1 1 B DC 13 1_555 C DG 1 1_555 0.273 -0.005 -0.071 14.465 -14.451 4.603 12 B_DC13:DG1_C B 13 ? C 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 B DG 1 1_555 C DC 13 1_555 B DT 2 1_555 C DA 12 1_555 -1.046 -0.787 2.883 -0.374 2.203 30.654 -1.862 1.910 2.833 4.160 0.706 30.733 1 BB_DG1DT2:DA12DC13_CC B 1 ? C 13 ? B 2 ? C 12 ? 1 B DT 2 1_555 C DA 12 1_555 B DC 3 1_555 C DG 11 1_555 0.784 0.070 3.078 3.127 3.926 40.423 -0.312 -0.798 3.121 5.655 -4.505 40.721 2 BB_DT2DC3:DG11DA12_CC B 2 ? C 12 ? B 3 ? C 11 ? 1 B DC 3 1_555 C DG 11 1_555 B DA 4 1_555 C DT 10 1_555 0.010 0.397 3.263 0.525 10.570 30.811 -1.174 0.075 3.221 19.197 -0.953 32.536 3 BB_DC3DA4:DT10DG11_CC B 3 ? C 11 ? B 4 ? C 10 ? 1 B DA 4 1_555 C DT 10 1_555 B DC 5 1_555 C DG 9 1_555 0.519 -0.574 3.171 -0.794 1.974 29.367 -1.535 -1.185 3.111 3.887 1.564 29.442 4 BB_DA4DC5:DG9DT10_CC B 4 ? C 10 ? B 5 ? C 9 ? 1 B DC 5 1_555 C DG 9 1_555 B DT 6 1_555 C DA 8 1_555 -0.191 -0.382 3.435 4.160 7.246 29.970 -2.149 1.180 3.203 13.680 -7.855 31.087 5 BB_DC5DT6:DA8DG9_CC B 5 ? C 9 ? B 6 ? C 8 ? 1 B DT 6 1_555 C DA 8 1_555 B DA 7 1_555 C DT 7 1_555 0.290 0.008 3.480 2.196 5.817 36.837 -0.808 -0.143 3.452 9.125 -3.445 37.340 6 BB_DT6DA7:DT7DA8_CC B 6 ? C 8 ? B 7 ? C 7 ? 1 B DA 7 1_555 C DT 7 1_555 B DC 8 1_555 C DG 6 1_555 -0.266 -0.370 3.346 -2.082 4.750 33.900 -1.387 0.118 3.275 8.087 3.545 34.283 7 BB_DA7DC8:DG6DT7_CC B 7 ? C 7 ? B 8 ? C 6 ? 1 B DC 8 1_555 C DG 6 1_555 B 5CM 9 1_555 C DG 5 1_555 0.661 0.166 3.074 4.744 0.138 29.785 0.292 -0.347 3.139 0.267 -9.155 30.152 8 BB_DC85CM9:DG5DG6_CC B 8 ? C 6 ? B 9 ? C 5 ? 1 B 5CM 9 1_555 C DG 5 1_555 B DG 11 1_555 C DC 3 1_555 0.487 -0.080 6.650 -12.511 -3.637 65.290 0.220 -1.455 6.471 -3.336 11.477 66.436 9 BB_5CM9DG11:DC3DG5_CC B 9 ? C 5 ? B 11 ? C 3 ? 1 B DG 11 1_555 C DC 3 1_555 B DA 12 1_555 C DT 2 1_555 -1.268 -0.970 3.451 -8.451 4.098 34.981 -2.187 0.751 3.521 6.670 13.755 36.182 10 BB_DG11DA12:DT2DC3_CC B 11 ? C 3 ? B 12 ? C 2 ? 1 B DA 12 1_555 C DT 2 1_555 B DC 13 1_555 C DG 1 1_555 0.434 -1.287 3.455 1.479 3.070 33.819 -2.713 -0.497 3.344 5.261 -2.535 33.986 11 BB_DA12DC13:DG1DT2_CC B 12 ? C 2 ? B 13 ? C 1 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 4 'ACETATE ION' ACT 5 1,2-ETHANEDIOL EDO 6 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 3VXV _pdbx_initial_refinement_model.details 'PDB ENTRY 3VXV' #