data_3HGD # _entry.id 3HGD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 3HGD pdb_00003hgd 10.2210/pdb3hgd/pdb NDB NA0003 ? ? RCSB RCSB053100 ? ? WWPDB D_1000053100 ? ? # 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 2009-08-18 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-11-01 4 'Structure model' 1 3 2024-02-21 # _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' # 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' struct_conn # 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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.entry_id 3HGD _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2009-05-13 _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_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3HG8 . unspecified PDB 3HGA . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Sheng, J.' 1 'Hassan, A.E.' 2 'Zhang, W.' 3 'Huang, Z.' 4 # _citation.id primary _citation.title 'High fidelity of base pairing by 2-selenothymidine in DNA.' _citation.journal_abbrev J.Am.Chem.Soc. _citation.journal_volume 132 _citation.page_first 2120 _citation.page_last 2121 _citation.year 2010 _citation.journal_id_ASTM JACSAT _citation.country US _citation.journal_id_ISSN 0002-7863 _citation.journal_id_CSD 0004 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20108896 _citation.pdbx_database_id_DOI 10.1021/ja909330m # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Hassan, A.E.' 1 ? primary 'Sheng, J.' 2 ? primary 'Zhang, W.' 3 ? primary 'Huang, Z.' 4 ? # 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*(UMS)P*GP*(US3)P*AP*CP*AP*C)-3'" 2568.538 2 ? ? ? '2-Se-Thymidine containing DNA' 2 water nat water 18.015 35 ? ? ? ? # _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)(UMS)(DG)(US3)(DA)(DC)(DA)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GUGTACAC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # 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 UMS n 1 3 DG n 1 4 US3 n 1 5 DA n 1 6 DC n 1 7 DA n 1 8 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 'the 2-Se-thymidine residue was chemically synthesized and incorporated into DNA oligonucleotide through solid phase synthesis' # 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 HOH non-polymer . WATER ? 'H2 O' 18.015 UMS 'DNA linking' n "2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE" ? 'C10 H15 N2 O8 P Se' 401.168 US3 'DNA linking' n '1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methyl-2-selanylpyrimidin-4(1H)-one' "2-Se-Thymidine-5'-phosphate" 'C10 H15 N2 O7 P Se' 385.169 # 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 1 1 DG DG A . n A 1 2 UMS 2 2 2 UMS UMS A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 US3 4 4 4 US3 US3 A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DC 6 6 6 DC DC A . n A 1 7 DA 7 7 7 DA DA A . n A 1 8 DC 8 8 8 DC DC A . n B 1 1 DG 1 1 1 DG DG B . n B 1 2 UMS 2 2 2 UMS UMS B . n B 1 3 DG 3 3 3 DG DG B . n B 1 4 US3 4 4 4 US3 US3 B . n B 1 5 DA 5 5 5 DA DA B . n B 1 6 DC 6 6 6 DC DC B . n B 1 7 DA 7 7 7 DA DA B . n B 1 8 DC 8 8 8 DC DC 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 HOH 1 24 24 HOH HOH A . C 2 HOH 2 31 31 HOH HOH A . C 2 HOH 3 35 35 HOH HOH A . C 2 HOH 4 38 38 HOH HOH A . C 2 HOH 5 41 41 HOH HOH A . C 2 HOH 6 46 46 HOH HOH A . C 2 HOH 7 50 50 HOH HOH A . C 2 HOH 8 60 60 HOH HOH A . C 2 HOH 9 69 69 HOH HOH A . C 2 HOH 10 71 71 HOH HOH A . C 2 HOH 11 80 80 HOH HOH A . C 2 HOH 12 88 88 HOH HOH A . D 2 HOH 1 12 12 HOH HOH B . D 2 HOH 2 13 13 HOH HOH B . D 2 HOH 3 14 14 HOH HOH B . D 2 HOH 4 22 22 HOH HOH B . D 2 HOH 5 23 23 HOH HOH B . D 2 HOH 6 26 26 HOH HOH B . D 2 HOH 7 30 30 HOH HOH B . D 2 HOH 8 32 32 HOH HOH B . D 2 HOH 9 33 33 HOH HOH B . D 2 HOH 10 36 36 HOH HOH B . D 2 HOH 11 37 37 HOH HOH B . D 2 HOH 12 39 39 HOH HOH B . D 2 HOH 13 44 44 HOH HOH B . D 2 HOH 14 45 45 HOH HOH B . D 2 HOH 15 48 48 HOH HOH B . D 2 HOH 16 53 53 HOH HOH B . D 2 HOH 17 58 58 HOH HOH B . D 2 HOH 18 59 59 HOH HOH B . D 2 HOH 19 64 64 HOH HOH B . D 2 HOH 20 72 72 HOH HOH B . D 2 HOH 21 76 76 HOH HOH B . D 2 HOH 22 83 83 HOH HOH B . D 2 HOH 23 90 90 HOH HOH B . # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 DENZO . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data reduction' http://www.hkl-xray.com/ ? ? 2 SCALEPACK . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 3 CNS . ? package 'Axel T. Brunger' axel.brunger@yale.edu refinement http://cns-online.org/ Fortran_77 ? 4 PDB_EXTRACT 3.005 'June 11, 2008' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 5 CBASS . ? ? ? ? 'data collection' ? ? ? 6 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 7 HKL-2000 . ? ? ? ? 'data scaling' ? ? ? 8 CNS . ? ? ? ? phasing ? ? ? # _cell.entry_id 3HGD _cell.length_a 45.828 _cell.length_b 45.828 _cell.length_c 42.501 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _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 3HGD _symmetry.space_group_name_H-M 'P 61' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3HGD _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.51 _exptl_crystal.density_percent_sol 50.96 _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 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details 'MPD,sodium cacodylate,spermine tetra-HCl, vapor diffusion, hanging drop, temperature 298K' # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC Q210' _diffrn_detector.pdbx_collection_date 2008-12-07 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ? _diffrn_radiation.monochromator 'Si(111)' _diffrn_radiation.pdbx_diffrn_protocol SAD _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9795 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X12C' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X12C _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9795 # _reflns.entry_id 3HGD _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50.000 _reflns.d_resolution_high 1.570 _reflns.number_obs 6839 _reflns.number_all ? _reflns.percent_possible_obs 95.100 _reflns.pdbx_Rmerge_I_obs 0.091 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 21.159 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 17.000 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _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 1.57 1.64 74.90 0.607 ? ? 6.60 ? ? ? ? ? ? ? 1 1.64 1.70 85.30 0.419 ? ? 8.70 ? ? ? ? ? ? ? 2 1.70 1.78 96.30 0.271 ? ? 11.10 ? ? ? ? ? ? ? 3 1.78 1.87 100.00 0.229 ? ? 15.50 ? ? ? ? ? ? ? 4 1.87 1.99 100.00 0.192 ? ? 21.40 ? ? ? ? ? ? ? 5 1.99 2.14 100.00 0.161 ? ? 21.70 ? ? ? ? ? ? ? 6 2.14 2.36 100.00 0.142 ? ? 21.70 ? ? ? ? ? ? ? 7 2.36 2.70 100.00 0.118 ? ? 21.70 ? ? ? ? ? ? ? 8 2.70 3.40 99.60 0.088 ? ? 20.90 ? ? ? ? ? ? ? 9 3.40 50.00 94.80 0.071 ? ? 16.80 ? ? ? ? ? ? ? 10 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 3HGD _refine.ls_number_reflns_obs 6688 _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 50.000 _refine.ls_d_res_high 1.570 _refine.ls_percent_reflns_obs 93.300 _refine.ls_R_factor_obs 0.204 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.204 _refine.ls_R_factor_R_free 0.220 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.100 _refine.ls_number_reflns_R_free 725 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min 0.70 _refine.occupancy_max 1.00 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 27.420 _refine.aniso_B[1][1] 0.090 _refine.aniso_B[2][2] 0.090 _refine.aniso_B[3][3] -0.179 _refine.aniso_B[1][2] 0.292 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol 56.701 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _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 ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _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_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 324 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 35 _refine_hist.number_atoms_total 359 _refine_hist.d_res_high 1.570 _refine_hist.d_res_low 50.000 # 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 c_bond_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it 0.000 1.500 ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it 0.000 2.000 ? ? 'X-RAY DIFFRACTION' ? c_scbond_it 1.567 2.000 ? ? 'X-RAY DIFFRACTION' ? c_scangle_it 2.266 2.500 ? ? 'X-RAY DIFFRACTION' ? # loop_ _pdbx_xplor_file.pdbx_refine_id _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file 'X-RAY DIFFRACTION' 1 dna-rna_rep_jia.param ? 'X-RAY DIFFRACTION' 2 CNS_TOPPAR:water_rep.param ? # _struct.entry_id 3HGD _struct.title 'Crystal Structure of 2-Se-Thymidine Derivatized DNA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3HGD _struct_keywords.text '2-Se-thymidine DNA, DNA' _struct_keywords.pdbx_keywords 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 2 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3HGD _struct_ref.pdbx_db_accession 3HGD _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code GUGUACAC _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 3HGD A 1 ? 8 ? 3HGD 1 ? 8 ? 1 8 2 1 3HGD B 1 ? 8 ? 3HGD 1 ? 8 ? 1 8 # _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 # 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)' 1920 ? 1 MORE 6 ? 1 'SSA (A^2)' 2850 ? # _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 # _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 # _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 DG 1 "O3'" ? ? ? 1_555 A UMS 2 P ? ? A DG 1 A UMS 2 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale2 covale both ? A UMS 2 "O3'" ? ? ? 1_555 A DG 3 P ? ? A UMS 2 A DG 3 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale3 covale both ? A DG 3 "O3'" ? ? ? 1_555 A US3 4 P ? ? A DG 3 A US3 4 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale4 covale one ? A US3 4 "O3'" ? ? ? 1_555 A DA 5 P ? ? A US3 4 A DA 5 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale5 covale both ? B DG 1 "O3'" ? ? ? 1_555 B UMS 2 P ? ? B DG 1 B UMS 2 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale6 covale both ? B UMS 2 "O3'" ? ? ? 1_555 B DG 3 P ? ? B UMS 2 B DG 3 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale7 covale both ? B DG 3 "O3'" ? ? ? 1_555 B US3 4 P ? ? B DG 3 B US3 4 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale8 covale one ? B US3 4 "O3'" ? ? ? 1_555 B DA 5 P ? ? B US3 4 B DA 5 1_555 ? ? ? ? ? ? ? 1.604 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 1 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 1 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 1 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A UMS 2 N3 ? ? ? 1_555 B DA 7 N1 ? ? A UMS 2 B DA 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A UMS 2 O4 ? ? ? 1_555 B DA 7 N6 ? ? A UMS 2 B DA 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 6 N3 ? ? A DG 3 B DC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 6 O2 ? ? A DG 3 B DC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 6 N4 ? ? A DG 3 B DC 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A US3 4 N3 ? ? ? 1_555 B DA 5 N1 ? ? A US3 4 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A US3 4 O4 ? ? ? 1_555 B DA 5 N6 ? ? A US3 4 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B US3 4 N3 ? ? A DA 5 B US3 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B US3 4 O4 ? ? A DA 5 B US3 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 6 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 6 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 6 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 6 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 6 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 6 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B UMS 2 N3 ? ? A DA 7 B UMS 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B UMS 2 O4 ? ? A DA 7 B UMS 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 8 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 8 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 8 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # 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 UMS 2 A UMS 2 ? DU ? 2 A US3 4 A US3 4 ? DT ? 3 B UMS 2 B UMS 2 ? DU ? 4 B US3 4 B US3 4 ? DT ? # _phasing.method MR # 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 HOH O O N N 108 HOH H1 H N N 109 HOH H2 H N N 110 UMS OP3 O N N 111 UMS P P N N 112 UMS OP1 O N N 113 UMS OP2 O N N 114 UMS "O5'" O N N 115 UMS "C5'" C N N 116 UMS "C4'" C N R 117 UMS "O4'" O N N 118 UMS "C3'" C N R 119 UMS "O3'" O N N 120 UMS "C2'" C N R 121 UMS "SE2'" SE N N 122 UMS "C1'" C N R 123 UMS "CA'" C N N 124 UMS N1 N N N 125 UMS C2 C N N 126 UMS O2 O N N 127 UMS N3 N N N 128 UMS C4 C N N 129 UMS O4 O N N 130 UMS C5 C N N 131 UMS C6 C N N 132 UMS HOP3 H N N 133 UMS HOP2 H N N 134 UMS "H5'" H N N 135 UMS "H5'2" H N N 136 UMS "H4'" H N N 137 UMS "H3'" H N N 138 UMS "HO3'" H N N 139 UMS "H2'" H N N 140 UMS "H1'" H N N 141 UMS "HA'" H N N 142 UMS "HA'2" H N N 143 UMS "HA'3" H N N 144 UMS H3 H N N 145 UMS H5 H N N 146 UMS H6 H N N 147 US3 P P N N 148 US3 N1 N N N 149 US3 C2 C N N 150 US3 SE2 SE N N 151 US3 N3 N N N 152 US3 C4 C N N 153 US3 O4 O N N 154 US3 C5 C N N 155 US3 C6 C N N 156 US3 "C1'" C N R 157 US3 OP3 O N N 158 US3 "C2'" C N N 159 US3 OP2 O N N 160 US3 "C3'" C N S 161 US3 "O3'" O N N 162 US3 "C4'" C N R 163 US3 "O4'" O N N 164 US3 "C5'" C N N 165 US3 "O5'" O N N 166 US3 C5A C N N 167 US3 H6 H N N 168 US3 "H1'" H N N 169 US3 HOP3 H N N 170 US3 "H2'" H N N 171 US3 "H2'A" H N N 172 US3 HOP2 H N N 173 US3 "H3'" H N N 174 US3 "HO3'" H N N 175 US3 "H4'" H N N 176 US3 "H5'" H N N 177 US3 "H5'A" H N N 178 US3 H5A H N N 179 US3 H5AA H N N 180 US3 H5AB H N N 181 US3 HSE2 H N N 182 US3 OP1 O N N 183 # 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 HOH O H1 sing N N 113 HOH O H2 sing N N 114 UMS OP3 P sing N N 115 UMS OP3 HOP3 sing N N 116 UMS P OP1 doub N N 117 UMS P OP2 sing N N 118 UMS P "O5'" sing N N 119 UMS OP2 HOP2 sing N N 120 UMS "O5'" "C5'" sing N N 121 UMS "C5'" "C4'" sing N N 122 UMS "C5'" "H5'" sing N N 123 UMS "C5'" "H5'2" sing N N 124 UMS "C4'" "O4'" sing N N 125 UMS "C4'" "C3'" sing N N 126 UMS "C4'" "H4'" sing N N 127 UMS "O4'" "C1'" sing N N 128 UMS "C3'" "O3'" sing N N 129 UMS "C3'" "C2'" sing N N 130 UMS "C3'" "H3'" sing N N 131 UMS "O3'" "HO3'" sing N N 132 UMS "C2'" "SE2'" sing N N 133 UMS "C2'" "C1'" sing N N 134 UMS "C2'" "H2'" sing N N 135 UMS "SE2'" "CA'" sing N N 136 UMS "C1'" N1 sing N N 137 UMS "C1'" "H1'" sing N N 138 UMS "CA'" "HA'" sing N N 139 UMS "CA'" "HA'2" sing N N 140 UMS "CA'" "HA'3" sing N N 141 UMS N1 C2 sing N N 142 UMS N1 C6 sing N N 143 UMS C2 O2 doub N N 144 UMS C2 N3 sing N N 145 UMS N3 C4 sing N N 146 UMS N3 H3 sing N N 147 UMS C4 O4 doub N N 148 UMS C4 C5 sing N N 149 UMS C5 C6 doub N N 150 UMS C5 H5 sing N N 151 UMS C6 H6 sing N N 152 US3 P OP2 sing N N 153 US3 N1 "C1'" sing N N 154 US3 N1 C6 sing N N 155 US3 C2 N1 sing N N 156 US3 C2 N3 doub N N 157 US3 SE2 C2 sing N N 158 US3 SE2 HSE2 sing N N 159 US3 N3 C4 sing N N 160 US3 C4 O4 doub N N 161 US3 C4 C5 sing N N 162 US3 C5 C5A sing N N 163 US3 C6 C5 doub N N 164 US3 C6 H6 sing N N 165 US3 "C1'" "O4'" sing N N 166 US3 "C1'" "H1'" sing N N 167 US3 OP3 P sing N N 168 US3 OP3 HOP3 sing N N 169 US3 "C2'" "C1'" sing N N 170 US3 "C2'" "C3'" sing N N 171 US3 "C2'" "H2'" sing N N 172 US3 "C2'" "H2'A" sing N N 173 US3 OP2 HOP2 sing N N 174 US3 "C3'" "C4'" sing N N 175 US3 "C3'" "H3'" sing N N 176 US3 "O3'" "C3'" sing N N 177 US3 "O3'" "HO3'" sing N N 178 US3 "C4'" "O4'" sing N N 179 US3 "C4'" "C5'" sing N N 180 US3 "C4'" "H4'" sing N N 181 US3 "C5'" "O5'" sing N N 182 US3 "C5'" "H5'" sing N N 183 US3 "C5'" "H5'A" sing N N 184 US3 "O5'" P sing N N 185 US3 C5A H5A sing N N 186 US3 C5A H5AA sing N N 187 US3 C5A H5AB sing N N 188 US3 P OP1 doub N N 189 # _ndb_struct_conf_na.entry_id 3HGD _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 8 1_555 -0.341 -0.071 0.054 -10.209 -9.207 0.845 1 A_DG1:DC8_B A 1 ? B 8 ? 19 1 1 A UMS 2 1_555 B DA 7 1_555 -0.058 -0.146 0.016 2.182 -9.743 -1.421 2 A_UMS2:DA7_B A 2 ? B 7 ? 20 1 1 A DG 3 1_555 B DC 6 1_555 -0.334 -0.111 0.217 -0.153 -12.407 0.199 3 A_DG3:DC6_B A 3 ? B 6 ? 19 1 1 A US3 4 1_555 B DA 5 1_555 -0.348 -0.077 0.050 2.431 -11.951 -3.793 4 A_US34:DA5_B A 4 ? B 5 ? 20 1 1 A DA 5 1_555 B US3 4 1_555 0.166 -0.149 0.043 1.588 -13.604 -0.712 5 A_DA5:US34_B A 5 ? B 4 ? 20 1 1 A DC 6 1_555 B DG 3 1_555 0.139 -0.229 0.224 1.031 -9.295 0.605 6 A_DC6:DG3_B A 6 ? B 3 ? 19 1 1 A DA 7 1_555 B UMS 2 1_555 0.117 -0.074 0.160 7.839 -9.333 1.841 7 A_DA7:UMS2_B A 7 ? B 2 ? 20 1 1 A DC 8 1_555 B DG 1 1_555 0.246 -0.093 -0.318 20.886 -12.222 -0.297 8 A_DC8:DG1_B A 8 ? B 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 A DG 1 1_555 B DC 8 1_555 A UMS 2 1_555 B DA 7 1_555 -0.721 -1.034 3.009 -1.197 7.270 33.408 -2.783 1.058 2.753 12.459 2.052 34.189 1 AA_DG1UMS2:DA7DC8_BB A 1 ? B 8 ? A 2 ? B 7 ? 1 A UMS 2 1_555 B DA 7 1_555 A DG 3 1_555 B DC 6 1_555 0.081 -1.636 3.221 -2.635 8.466 29.557 -4.589 -0.623 2.645 16.143 5.024 30.830 2 AA_UMS2DG3:DC6DA7_BB A 2 ? B 7 ? A 3 ? B 6 ? 1 A DG 3 1_555 B DC 6 1_555 A US3 4 1_555 B DA 5 1_555 -0.922 -1.699 3.232 -0.269 8.001 33.277 -4.065 1.528 2.768 13.726 0.461 34.200 3 AA_DG3US34:DA5DC6_BB A 3 ? B 6 ? A 4 ? B 5 ? 1 A US3 4 1_555 B DA 5 1_555 A DA 5 1_555 B US3 4 1_555 0.261 -1.162 3.239 0.141 11.699 30.751 -3.918 -0.439 2.634 21.127 -0.255 32.852 4 AA_US34DA5:US34DA5_BB A 4 ? B 5 ? A 5 ? B 4 ? 1 A DA 5 1_555 B US3 4 1_555 A DC 6 1_555 B DG 3 1_555 0.204 -1.641 3.304 -1.564 6.532 36.108 -3.468 -0.531 2.961 10.426 2.497 36.707 5 AA_DA5DC6:DG3US34_BB A 5 ? B 4 ? A 6 ? B 3 ? 1 A DC 6 1_555 B DG 3 1_555 A DA 7 1_555 B UMS 2 1_555 -0.279 -1.475 3.023 0.164 9.001 28.557 -4.456 0.570 2.453 17.700 -0.323 29.914 6 AA_DC6DA7:UMS2DG3_BB A 6 ? B 3 ? A 7 ? B 2 ? 1 A DA 7 1_555 B UMS 2 1_555 A DC 8 1_555 B DG 1 1_555 -0.087 -1.036 3.048 2.289 9.187 30.272 -3.398 0.533 2.616 17.074 -4.255 31.685 7 AA_DA7DC8:DG1UMS2_BB A 7 ? B 2 ? A 8 ? B 1 ? # _atom_sites.entry_id 3HGD _atom_sites.fract_transf_matrix[1][1] 0.021821 _atom_sites.fract_transf_matrix[1][2] 0.012598 _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] 0.025196 _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] 0.023529 _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 SE # loop_