data_3EY2 # _entry.id 3EY2 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.378 _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 3EY2 pdb_00003ey2 10.2210/pdb3ey2/pdb NDB AD0074 ? ? RCSB RCSB049910 ? ? WWPDB D_1000049910 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3EY2 . unspecified PDB 3EY3 . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3EY2 _pdbx_database_status.recvd_initial_deposition_date 2008-10-17 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Egli, M.' 1 'Pallan, P.S.' 2 # _citation.id primary _citation.title ;A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution. ; _citation.journal_abbrev 'Chem.Commun.(Camb.)' _citation.journal_volume 15 _citation.page_first 2017 _citation.page_last 2019 _citation.year 2009 _citation.journal_id_ASTM ? _citation.country UK _citation.journal_id_ISSN 1359-7345 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19333476 _citation.pdbx_database_id_DOI 10.1039/b822781k # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Pallan, P.S.' 1 ? primary 'Prakash, T.P.' 2 ? primary 'Li, F.' 3 ? primary 'Eoff, R.L.' 4 ? primary 'Manoharan, M.' 5 ? primary 'Egli, M.' 6 ? # _cell.entry_id 3EY2 _cell.length_a 24.690 _cell.length_b 42.920 _cell.length_c 46.120 _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 3EY2 _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _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 syn "5'-D(*GP*CP*GP*TP*AP*(USM)P*AP*CP*GP*C)-3'" 3077.070 2 ? ? ? ? 2 non-polymer syn N-methylpropane-1,3-diamine 88.151 1 ? ? ? ? 3 water nat water 18.015 133 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DG)(DC)(DG)(DT)(DA)(USM)(DA)(DC)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GCGTAUACGC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DC n 1 3 DG n 1 4 DT n 1 5 DA n 1 6 USM n 1 7 DA n 1 8 DC n 1 9 DG n 1 10 DC n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'Chemically synthesized modified DNA (oligonucleotide)' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3EY2 _struct_ref.pdbx_db_accession 3EY2 _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code GCGTAUACGC _struct_ref.pdbx_db_isoform ? # 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 3EY2 A 1 ? 10 ? 3EY2 101 ? 110 ? 101 110 2 1 3EY2 B 1 ? 10 ? 3EY2 201 ? 210 ? 201 210 # 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 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 HOH non-polymer . WATER ? 'H2 O' 18.015 N3D non-polymer . N-methylpropane-1,3-diamine ? 'C4 H12 N2' 88.151 USM 'DNA linking' n ;2'-S-methyl-2'-thiouridine 5'-(dihydrogen phosphate) ; ? 'C10 H15 N2 O8 P S' 354.273 # _exptl.entry_id 3EY2 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.99 _exptl_crystal.density_percent_sol 38.05 _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 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;5% MPD, 20 mM Sodium Cacodylate (pH 7.0), 6 mM Spermine tetra-HCl, 40 mM Potassium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K ; _exptl_crystal_grow.pdbx_pH_range ? # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 MPD ? ? ? 1 2 1 'Sodium Cacodylate' ? ? ? 1 3 1 'Spermine tetra-HCl' ? ? ? 1 4 1 'Potassium Chloride' ? ? ? 1 5 2 MPD ? ? ? 1 6 2 'Sodium Cacodylate' ? ? ? 1 7 2 'Spermine tetra-HCl' ? ? ? 1 8 2 'Potassium Chloride' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 120 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MARMOSAIC 225 mm CCD' _diffrn_detector.pdbx_collection_date 2006-03-06 _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 0.9788 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 5ID-B' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 5ID-B _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9788 # _reflns.entry_id 3EY2 _reflns.observed_criterion_sigma_I 0.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 30 _reflns.d_resolution_high 1.04 _reflns.number_obs 23179 _reflns.number_all 24305 _reflns.percent_possible_obs 95.4 _reflns.pdbx_Rmerge_I_obs 0.057 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 44.12 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _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_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.04 _reflns_shell.d_res_low 1.09 _reflns_shell.percent_possible_all ? _reflns_shell.Rmerge_I_obs 0.35 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 13.03 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 2774 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3EY2 _refine.ls_number_reflns_obs 22026 _refine.ls_number_reflns_all 23179 _refine.pdbx_ls_sigma_I 0.0 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 30 _refine.ls_d_res_high 1.04 _refine.ls_percent_reflns_obs 100 _refine.ls_R_factor_obs 0.1251 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1251 _refine.ls_R_factor_R_free 0.1526 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free 1158 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model 'PDB Entry 411D' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _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 ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _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 0 _refine_hist.pdbx_number_atoms_nucleic_acid 428 _refine_hist.pdbx_number_atoms_ligand 6 _refine_hist.number_atoms_solvent 133 _refine_hist.number_atoms_total 567 _refine_hist.d_res_high 1.04 _refine_hist.d_res_low 30 # 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_refine_id _refine_ls_restr.pdbx_restraint_function s_bond_d 0.016 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.031 ? ? ? 'X-RAY DIFFRACTION' ? # _struct.entry_id 3EY2 _struct.title ;A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3EY2 _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;2'-Thiomethyl modified DNA, modified sugar, nucleic acid structure., DNA ; # 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 1 ? C N N 2 ? D N N 3 ? E N N 3 ? # _struct_biol.id 1 _struct_biol.details ? # 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 covale1 covale both ? A DA 5 "O3'" ? ? ? 1_555 A USM 6 P ? ? A DA 105 A USM 106 1_555 ? ? ? ? ? ? ? 1.579 ? ? covale2 covale both ? A USM 6 "O3'" ? ? ? 1_555 A DA 7 P ? ? A USM 106 A DA 107 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale3 covale both ? B DA 5 "O3'" ? ? ? 1_555 B USM 6 P ? ? B DA 205 B USM 206 1_555 ? ? ? ? ? ? ? 1.593 ? ? covale4 covale both ? B USM 6 "O3'" ? ? ? 1_555 B DA 7 P ? ? B USM 206 B DA 207 1_555 ? ? ? ? ? ? ? 1.600 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 101 B DC 210 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 101 B DC 210 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 101 B DC 210 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 102 B DG 209 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 102 B DG 209 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 102 B DG 209 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 8 N3 A ? A DG 103 B DC 208 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 8 O2 A ? A DG 103 B DC 208 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 8 N4 A ? A DG 103 B DC 208 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 104 B DA 207 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 104 B DA 207 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B USM 6 N3 ? ? A DA 105 B USM 206 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B USM 6 O4 ? ? A DA 105 B USM 206 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A USM 6 N3 ? ? ? 1_555 B DA 5 N1 ? ? A USM 106 B DA 205 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A USM 6 O4 ? ? ? 1_555 B DA 5 N6 ? ? A USM 106 B DA 205 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 107 B DT 204 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 107 B DT 204 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 108 B DG 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 108 B DG 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 108 B DG 203 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 109 B DC 202 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 109 B DC 202 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 109 B DC 202 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 110 B DG 201 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 110 B DG 201 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 110 B DG 201 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id B _struct_site.pdbx_auth_comp_id N3D _struct_site.pdbx_auth_seq_id 501 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 7 _struct_site.details 'BINDING SITE FOR RESIDUE N3D B 501' # 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 7 DG A 9 ? DG A 109 . ? 3_645 ? 2 AC1 7 HOH D . ? HOH A 354 . ? 1_455 ? 3 AC1 7 HOH D . ? HOH A 359 . ? 3_645 ? 4 AC1 7 HOH D . ? HOH A 380 . ? 1_455 ? 5 AC1 7 DG B 3 ? DG B 203 . ? 2_564 ? 6 AC1 7 DT B 4 ? DT B 204 . ? 2_564 ? 7 AC1 7 DG B 9 ? DG B 209 . ? 1_555 ? # _database_PDB_matrix.entry_id 3EY2 _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 3EY2 _atom_sites.fract_transf_matrix[1][1] 0.040502 _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] 0.023299 _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] 0.021683 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # 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 DG 1 101 101 DG GUA A . n A 1 2 DC 2 102 102 DC CYT A . n A 1 3 DG 3 103 103 DG GUA A . n A 1 4 DT 4 104 104 DT THY A . n A 1 5 DA 5 105 105 DA ADE A . n A 1 6 USM 6 106 106 USM USM A . n A 1 7 DA 7 107 107 DA ADE A . n A 1 8 DC 8 108 108 DC CYT A . n A 1 9 DG 9 109 109 DG GUA A . n A 1 10 DC 10 110 110 DC CYT A . n B 1 1 DG 1 201 201 DG GUA B . n B 1 2 DC 2 202 202 DC CYT B . n B 1 3 DG 3 203 203 DG GUA B . n B 1 4 DT 4 204 204 DT THY B . n B 1 5 DA 5 205 205 DA ADE B . n B 1 6 USM 6 206 206 USM USM B . n B 1 7 DA 7 207 207 DA ADE B . n B 1 8 DC 8 208 208 DC CYT B . n B 1 9 DG 9 209 209 DG GUA B . n B 1 10 DC 10 210 210 DC CYT B . 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 C 2 N3D 1 501 501 N3D N3D B . D 3 HOH 1 301 301 HOH HOH A . D 3 HOH 2 305 305 HOH HOH A . D 3 HOH 3 309 309 HOH HOH A . D 3 HOH 4 310 310 HOH HOH A . D 3 HOH 5 311 311 HOH HOH A . D 3 HOH 6 312 312 HOH HOH A . D 3 HOH 7 319 319 HOH HOH A . D 3 HOH 8 321 321 HOH HOH A . D 3 HOH 9 328 328 HOH HOH A . D 3 HOH 10 331 331 HOH HOH A . D 3 HOH 11 332 332 HOH HOH A . D 3 HOH 12 333 333 HOH HOH A . D 3 HOH 13 334 334 HOH HOH A . D 3 HOH 14 336 336 HOH HOH A . D 3 HOH 15 337 337 HOH HOH A . D 3 HOH 16 342 342 HOH HOH A . D 3 HOH 17 343 343 HOH HOH A . D 3 HOH 18 344 344 HOH HOH A . D 3 HOH 19 346 346 HOH HOH A . D 3 HOH 20 347 347 HOH HOH A . D 3 HOH 21 348 348 HOH HOH A . D 3 HOH 22 349 349 HOH HOH A . D 3 HOH 23 350 350 HOH HOH A . D 3 HOH 24 351 351 HOH HOH A . D 3 HOH 25 353 353 HOH HOH A . D 3 HOH 26 354 354 HOH HOH A . D 3 HOH 27 356 356 HOH HOH A . D 3 HOH 28 357 357 HOH HOH A . D 3 HOH 29 359 359 HOH HOH A . D 3 HOH 30 360 360 HOH HOH A . D 3 HOH 31 362 362 HOH HOH A . D 3 HOH 32 365 365 HOH HOH A . D 3 HOH 33 367 367 HOH HOH A . D 3 HOH 34 368 368 HOH HOH A . D 3 HOH 35 369 369 HOH HOH A . D 3 HOH 36 370 370 HOH HOH A . D 3 HOH 37 377 377 HOH HOH A . D 3 HOH 38 380 380 HOH HOH A . D 3 HOH 39 381 381 HOH HOH A . D 3 HOH 40 385 385 HOH HOH A . D 3 HOH 41 386 386 HOH HOH A . D 3 HOH 42 387 387 HOH HOH A . D 3 HOH 43 388 388 HOH HOH A . D 3 HOH 44 389 389 HOH HOH A . D 3 HOH 45 394 394 HOH HOH A . D 3 HOH 46 395 395 HOH HOH A . D 3 HOH 47 398 398 HOH HOH A . D 3 HOH 48 399 399 HOH HOH A . D 3 HOH 49 401 401 HOH HOH A . D 3 HOH 50 402 402 HOH HOH A . D 3 HOH 51 403 403 HOH HOH A . D 3 HOH 52 405 405 HOH HOH A . D 3 HOH 53 407 407 HOH HOH A . D 3 HOH 54 408 408 HOH HOH A . D 3 HOH 55 410 410 HOH HOH A . D 3 HOH 56 412 412 HOH HOH A . D 3 HOH 57 413 413 HOH HOH A . D 3 HOH 58 414 414 HOH HOH A . D 3 HOH 59 416 416 HOH HOH A . D 3 HOH 60 417 417 HOH HOH A . D 3 HOH 61 419 419 HOH HOH A . D 3 HOH 62 420 420 HOH HOH A . D 3 HOH 63 422 422 HOH HOH A . D 3 HOH 64 423 423 HOH HOH A . D 3 HOH 65 425 425 HOH HOH A . D 3 HOH 66 429 429 HOH HOH A . D 3 HOH 67 433 433 HOH HOH A . E 3 HOH 1 302 302 HOH HOH B . E 3 HOH 2 303 303 HOH HOH B . E 3 HOH 3 304 304 HOH HOH B . E 3 HOH 4 306 306 HOH HOH B . E 3 HOH 5 307 307 HOH HOH B . E 3 HOH 6 308 308 HOH HOH B . E 3 HOH 7 313 313 HOH HOH B . E 3 HOH 8 314 314 HOH HOH B . E 3 HOH 9 315 315 HOH HOH B . E 3 HOH 10 316 316 HOH HOH B . E 3 HOH 11 317 317 HOH HOH B . E 3 HOH 12 318 318 HOH HOH B . E 3 HOH 13 320 320 HOH HOH B . E 3 HOH 14 322 322 HOH HOH B . E 3 HOH 15 323 323 HOH HOH B . E 3 HOH 16 324 324 HOH HOH B . E 3 HOH 17 325 325 HOH HOH B . E 3 HOH 18 326 326 HOH HOH B . E 3 HOH 19 327 327 HOH HOH B . E 3 HOH 20 329 329 HOH HOH B . E 3 HOH 21 330 330 HOH HOH B . E 3 HOH 22 335 335 HOH HOH B . E 3 HOH 23 338 338 HOH HOH B . E 3 HOH 24 339 339 HOH HOH B . E 3 HOH 25 340 340 HOH HOH B . E 3 HOH 26 341 341 HOH HOH B . E 3 HOH 27 345 345 HOH HOH B . E 3 HOH 28 352 352 HOH HOH B . E 3 HOH 29 355 355 HOH HOH B . E 3 HOH 30 358 358 HOH HOH B . E 3 HOH 31 361 361 HOH HOH B . E 3 HOH 32 363 363 HOH HOH B . E 3 HOH 33 364 364 HOH HOH B . E 3 HOH 34 366 366 HOH HOH B . E 3 HOH 35 371 371 HOH HOH B . E 3 HOH 36 372 372 HOH HOH B . E 3 HOH 37 373 373 HOH HOH B . E 3 HOH 38 374 374 HOH HOH B . E 3 HOH 39 375 375 HOH HOH B . E 3 HOH 40 376 376 HOH HOH B . E 3 HOH 41 378 378 HOH HOH B . E 3 HOH 42 379 379 HOH HOH B . E 3 HOH 43 382 382 HOH HOH B . E 3 HOH 44 383 383 HOH HOH B . E 3 HOH 45 384 384 HOH HOH B . E 3 HOH 46 390 390 HOH HOH B . E 3 HOH 47 391 391 HOH HOH B . E 3 HOH 48 392 392 HOH HOH B . E 3 HOH 49 393 393 HOH HOH B . E 3 HOH 50 396 396 HOH HOH B . E 3 HOH 51 397 397 HOH HOH B . E 3 HOH 52 400 400 HOH HOH B . E 3 HOH 53 404 404 HOH HOH B . E 3 HOH 54 406 406 HOH HOH B . E 3 HOH 55 409 409 HOH HOH B . E 3 HOH 56 411 411 HOH HOH B . E 3 HOH 57 415 415 HOH HOH B . E 3 HOH 58 418 418 HOH HOH B . E 3 HOH 59 421 421 HOH HOH B . E 3 HOH 60 424 424 HOH HOH B . E 3 HOH 61 426 426 HOH HOH B . E 3 HOH 62 427 427 HOH HOH B . E 3 HOH 63 428 428 HOH HOH B . E 3 HOH 64 430 430 HOH HOH B . E 3 HOH 65 431 431 HOH HOH B . E 3 HOH 66 432 432 HOH HOH B . # 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 A USM 6 A USM 106 ? DU ? 2 B USM 6 B USM 206 ? DU ? # _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 # _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 # 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)' 1060 ? 1 MORE -3 ? 1 'SSA (A^2)' 3940 ? # _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 # 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 2009-04-28 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-10-25 4 'Structure model' 1 3 2023-09-06 # _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' 'Version format compliance' 2 3 'Structure model' 'Refinement description' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 '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' software 2 4 'Structure model' chem_comp_atom 3 4 'Structure model' chem_comp_bond 4 4 'Structure model' database_2 5 4 'Structure model' pdbx_initial_refinement_model 6 4 'Structure model' struct_conn 7 4 'Structure model' struct_ref_seq 8 4 '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' '_software.name' 2 4 'Structure model' '_database_2.pdbx_DOI' 3 4 'Structure model' '_database_2.pdbx_database_accession' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 4 'Structure model' '_struct_ref_seq.db_align_beg' 6 4 'Structure model' '_struct_ref_seq.db_align_end' 7 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 8 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 9 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MAR345 'data collection' . ? 1 MOLREP phasing . ? 2 SHELXL-97 refinement . ? 3 XDS 'data reduction' . ? 4 XDS 'data scaling' . ? 5 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "C2'" _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 DG _pdbx_validate_rmsd_bond.auth_seq_id_1 209 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 "C1'" _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 DG _pdbx_validate_rmsd_bond.auth_seq_id_2 209 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.452 _pdbx_validate_rmsd_bond.bond_target_value 1.518 _pdbx_validate_rmsd_bond.bond_deviation -0.066 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.010 _pdbx_validate_rmsd_bond.linker_flag N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DG 103 ? ? "C1'" A DG 103 ? ? "C2'" A DG 103 ? ? 110.63 106.80 3.83 0.50 N 2 1 "O4'" A DG 103 ? ? "C1'" A DG 103 ? ? N9 A DG 103 ? ? 103.17 108.00 -4.83 0.70 N 3 1 "O4'" A DA 107 ? ? "C1'" A DA 107 ? ? N9 A DA 107 ? ? 110.21 108.30 1.91 0.30 N 4 1 "O4'" A DC 108 ? ? "C1'" A DC 108 ? ? N1 A DC 108 ? ? 110.27 108.30 1.97 0.30 N 5 1 "O4'" B DG 203 ? ? "C1'" B DG 203 ? ? N9 B DG 203 ? ? 110.87 108.30 2.57 0.30 N 6 1 "O4'" B DT 204 ? ? "C1'" B DT 204 ? ? N1 B DT 204 ? ? 110.28 108.30 1.98 0.30 N 7 1 C4 B DT 204 ? ? C5 B DT 204 ? ? C7 B DT 204 ? ? 125.30 119.00 6.30 0.60 N 8 1 C6 B DT 204 ? ? C5 B DT 204 ? ? C7 B DT 204 ? ? 117.80 122.90 -5.10 0.60 N 9 1 "O4'" B DG 209 ? ? "C4'" B DG 209 ? A "C3'" B DG 209 ? A 101.97 104.50 -2.53 0.40 N 10 1 "O4'" B DG 209 ? ? "C1'" B DG 209 ? ? N9 B DG 209 ? ? 103.38 108.00 -4.62 0.70 N # 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 DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 N3D N1 N N N 147 N3D C2 C N N 148 N3D C3 C N N 149 N3D C4 C N N 150 N3D N5 N N N 151 N3D C6 C N N 152 N3D HN1 H N N 153 N3D HN1A H N N 154 N3D H2 H N N 155 N3D H2A H N N 156 N3D H3 H N N 157 N3D H3A H N N 158 N3D H4 H N N 159 N3D H4A H N N 160 N3D HN5 H N N 161 N3D H6 H N N 162 N3D H6A H N N 163 N3D H6B H N N 164 USM OP2 O N N 165 USM P P N N 166 USM OP1 O N N 167 USM OP3 O N N 168 USM "O5'" O N N 169 USM N1 N N N 170 USM C6 C N N 171 USM C2 C N N 172 USM O2 O N N 173 USM N3 N N N 174 USM C4 C N N 175 USM O4 O N N 176 USM C5 C N N 177 USM "C2'" C N R 178 USM "S2'" S N N 179 USM C2A C N N 180 USM "C5'" C N N 181 USM "C4'" C N R 182 USM "O4'" O N N 183 USM "C1'" C N R 184 USM "C3'" C N R 185 USM "O3'" O N N 186 USM HOP2 H N N 187 USM HOP3 H N N 188 USM H6 H N N 189 USM H5 H N N 190 USM "H2'" H N N 191 USM H2A H N N 192 USM H2AA H N N 193 USM H2AB H N N 194 USM "H5'" H N N 195 USM "H5'A" H N N 196 USM "H4'" H N N 197 USM "H1'" H N N 198 USM "H3'" H N N 199 USM "HO3'" H N N 200 USM HN3 H N N 201 # 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 DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 N3D N1 C2 sing N N 152 N3D C2 C3 sing N N 153 N3D C3 C4 sing N N 154 N3D C4 N5 sing N N 155 N3D N5 C6 sing N N 156 N3D N1 HN1 sing N N 157 N3D N1 HN1A sing N N 158 N3D C2 H2 sing N N 159 N3D C2 H2A sing N N 160 N3D C3 H3 sing N N 161 N3D C3 H3A sing N N 162 N3D C4 H4 sing N N 163 N3D C4 H4A sing N N 164 N3D N5 HN5 sing N N 165 N3D C6 H6 sing N N 166 N3D C6 H6A sing N N 167 N3D C6 H6B sing N N 168 USM P OP2 sing N N 169 USM OP2 HOP2 sing N N 170 USM OP1 P doub N N 171 USM "O5'" P sing N N 172 USM P OP3 sing N N 173 USM OP3 HOP3 sing N N 174 USM "C5'" "O5'" sing N N 175 USM C6 N1 sing N N 176 USM N1 C2 sing N N 177 USM N1 "C1'" sing N N 178 USM C5 C6 doub N N 179 USM C6 H6 sing N N 180 USM N3 C2 sing N N 181 USM C2 O2 doub N N 182 USM C4 N3 sing N N 183 USM C5 C4 sing N N 184 USM O4 C4 doub N N 185 USM C5 H5 sing N N 186 USM "C3'" "C2'" sing N N 187 USM "C2'" "C1'" sing N N 188 USM "C2'" "S2'" sing N N 189 USM "C2'" "H2'" sing N N 190 USM "S2'" C2A sing N N 191 USM C2A H2A sing N N 192 USM C2A H2AA sing N N 193 USM C2A H2AB sing N N 194 USM "C5'" "C4'" sing N N 195 USM "C5'" "H5'" sing N N 196 USM "C5'" "H5'A" sing N N 197 USM "C3'" "C4'" sing N N 198 USM "C4'" "O4'" sing N N 199 USM "C4'" "H4'" sing N N 200 USM "O4'" "C1'" sing N N 201 USM "C1'" "H1'" sing N N 202 USM "O3'" "C3'" sing N N 203 USM "C3'" "H3'" sing N N 204 USM "O3'" "HO3'" sing N N 205 USM N3 HN3 sing N N 206 # _ndb_struct_conf_na.entry_id 3EY2 _ndb_struct_conf_na.feature 'a-form double helix' # 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 A DG 1 1_555 B DC 10 1_555 -0.307 -0.127 0.210 4.374 -5.268 -1.586 1 A_DG101:DC210_B A 101 ? B 210 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.103 -0.121 0.202 4.341 -13.352 -0.694 2 A_DC102:DG209_B A 102 ? B 209 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.289 -0.102 -0.031 -8.607 -16.022 0.019 3 A_DG103:DC208_B A 103 ? B 208 ? 19 1 1 A DT 4 1_555 B DA 7 1_555 -0.167 -0.110 -0.008 -3.974 -17.836 -2.069 4 A_DT104:DA207_B A 104 ? B 207 ? 20 1 1 A DA 5 1_555 B USM 6 1_555 0.135 -0.074 0.114 -2.938 -14.904 -4.766 5 A_DA105:USM206_B A 105 ? B 206 ? 20 1 1 A USM 6 1_555 B DA 5 1_555 -0.073 -0.043 0.283 1.899 -13.595 7.173 6 A_USM106:DA205_B A 106 ? B 205 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 0.009 -0.102 0.029 5.652 -8.000 3.334 7 A_DA107:DT204_B A 107 ? B 204 ? 20 1 1 A DC 8 1_555 B DG 3 1_555 0.225 -0.130 -0.141 9.909 -10.091 0.245 8 A_DC108:DG203_B A 108 ? B 203 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 -0.199 -0.165 -0.043 -7.262 -9.348 0.482 9 A_DG109:DC202_B A 109 ? B 202 ? 19 1 1 A DC 10 1_555 B DG 1 1_555 0.194 -0.086 0.179 -3.861 5.320 -0.358 10 A_DC110:DG201_B A 110 ? B 201 ? 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 A DG 1 1_555 B DC 10 1_555 A DC 2 1_555 B DG 9 1_555 0.206 -1.472 3.267 0.726 0.118 40.231 -2.153 -0.217 3.266 0.171 -1.055 40.238 1 AA_DG101DC102:DG209DC210_BB A 101 ? B 210 ? A 102 ? B 209 ? 1 A DC 2 1_555 B DG 9 1_555 A DG 3 1_555 B DC 8 1_555 0.170 -2.118 3.450 1.647 9.624 26.002 -6.608 0.020 2.526 20.492 -3.507 27.746 2 AA_DC102DG103:DC208DG209_BB A 102 ? B 209 ? A 103 ? B 208 ? 1 A DG 3 1_555 B DC 8 1_555 A DT 4 1_555 B DA 7 1_555 -1.055 -1.343 2.993 -2.218 6.019 38.116 -2.693 1.351 2.811 9.137 3.367 38.633 3 AA_DG103DT104:DA207DC208_BB A 103 ? B 208 ? A 104 ? B 207 ? 1 A DT 4 1_555 B DA 7 1_555 A DA 5 1_555 B USM 6 1_555 0.555 -1.460 3.155 1.740 19.414 26.765 -5.321 -0.730 1.756 36.432 -3.266 33.005 4 AA_DT104DA105:USM206DA207_BB A 104 ? B 207 ? A 105 ? B 206 ? 1 A DA 5 1_555 B USM 6 1_555 A USM 6 1_555 B DA 5 1_555 0.960 -1.148 3.089 -0.014 9.251 32.691 -3.300 -1.646 2.673 16.039 0.024 33.941 5 AA_DA105USM106:DA205USM206_BB A 105 ? B 206 ? A 106 ? B 205 ? 1 A USM 6 1_555 B DA 5 1_555 A DA 7 1_555 B DT 4 1_555 -0.211 -1.415 2.983 -0.036 13.454 30.973 -4.251 0.358 2.197 23.834 0.064 33.703 6 AA_USM106DA107:DT204DA205_BB A 106 ? B 205 ? A 107 ? B 204 ? 1 A DA 7 1_555 B DT 4 1_555 A DC 8 1_555 B DG 3 1_555 -0.176 -2.057 3.286 -0.487 3.568 28.390 -4.944 0.250 3.013 7.237 0.988 28.613 7 AA_DA107DC108:DG203DT204_BB A 107 ? B 204 ? A 108 ? B 203 ? 1 A DC 8 1_555 B DG 3 1_555 A DG 9 1_555 B DC 2 1_555 -0.411 -2.050 3.583 -1.380 11.451 29.571 -5.835 0.502 2.642 21.436 2.583 31.694 8 AA_DC108DG109:DC202DG203_BB A 108 ? B 203 ? A 109 ? B 202 ? 1 A DG 9 1_555 B DC 2 1_555 A DC 10 1_555 B DG 1 1_555 0.195 -1.821 3.330 0.252 0.707 35.019 -3.134 -0.286 3.295 1.175 -0.418 35.027 9 AA_DG109DC110:DG201DC202_BB A 109 ? B 202 ? A 110 ? B 201 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 N-methylpropane-1,3-diamine N3D 3 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 411D _pdbx_initial_refinement_model.details 'PDB Entry 411D' #