data_1VTD # _entry.id 1VTD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _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 1VTD pdb_00001vtd 10.2210/pdb1vtd/pdb NDB BDL018 ? ? RCSB RCSB003037 ? ? WWPDB D_1000003037 ? ? # 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 2011-07-13 2 'Structure model' 1 1 2018-05-30 3 'Structure model' 1 2 2018-10-10 4 'Structure model' 1 3 2023-12-27 # _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' 'Data collection' 2 2 'Structure model' 'Source and taxonomy' 3 2 'Structure model' 'Structure summary' 4 3 'Structure model' 'Data collection' 5 3 'Structure model' 'Database references' 6 4 'Structure model' 'Data collection' 7 4 'Structure model' 'Database references' # 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 2 'Structure model' entity 2 2 'Structure model' pdbx_entity_src_syn 3 2 'Structure model' reflns 4 3 'Structure model' citation 5 3 'Structure model' citation_author 6 4 'Structure model' chem_comp_atom 7 4 'Structure model' chem_comp_bond 8 4 'Structure model' database_2 # 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 2 'Structure model' '_entity.src_method' 2 2 'Structure model' '_reflns.d_resolution_high' 3 2 'Structure model' '_reflns.d_resolution_low' 4 3 'Structure model' '_citation.journal_abbrev' 5 3 'Structure model' '_citation.pdbx_database_id_DOI' 6 3 'Structure model' '_citation.pdbx_database_id_PubMed' 7 3 'Structure model' '_citation.title' 8 3 'Structure model' '_citation_author.name' 9 4 'Structure model' '_database_2.pdbx_DOI' 10 4 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1VTD _pdbx_database_status.recvd_initial_deposition_date 1996-12-12 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Timsit, Y.' 1 'Westhof, E.' 2 'Fuchs, R.P.P.' 3 'Moras, D.' 4 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Unusual helical packing in crystals of DNA bearing a mutation hot spot.' Nature 341 459 462 1989 NATUAS UK 0028-0836 0006 ? 2797169 10.1038/341459a0 1 'Self-fitting and self-modifying properties of the B-DNA molecule.' 'J. Mol. Biol.' 251 629 647 1995 JMOBAK UK 0022-2836 0070 ? 7666416 10.1006/jmbi.1995.0461 2 'Base-pairing shift in the major groove of (CA)n tracts by B-DNA crystal structures.' Nature 354 167 170 1991 NATUAS UK 0028-0836 0006 ? 1944598 10.1038/354167a0 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Timsit, Y.' 1 ? primary 'Westhof, E.' 2 ? primary 'Fuchs, R.P.' 3 ? primary 'Moras, D.' 4 ? 1 'Timsit, Y.' 5 ? 1 'Moras, D.' 6 ? 2 'Timsit, Y.' 7 ? 2 'Vilbois, E.' 8 ? 2 'Moras, D.' 9 ? # 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 ;DNA (5'-D(*AP*CP*CP*GP*GP*CP*GP*CP*CP*AP*CP*A)-3') ; 3617.371 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(*TP*GP*TP*GP*GP*CP*GP*CP*CP*GP*GP*T)-3') ; 3710.401 1 ? ? ? ? # 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 polydeoxyribonucleotide no no '(DA)(DC)(DC)(DG)(DG)(DC)(DG)(DC)(DC)(DA)(DC)(DA)' ACCGGCGCCACA A ? 2 polydeoxyribonucleotide no no '(DT)(DG)(DT)(DG)(DG)(DC)(DG)(DC)(DC)(DG)(DG)(DT)' TGTGGCGCCGGT B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DA n 1 2 DC n 1 3 DC n 1 4 DG n 1 5 DG n 1 6 DC n 1 7 DG n 1 8 DC n 1 9 DC n 1 10 DA n 1 11 DC n 1 12 DA n 2 1 DT n 2 2 DG n 2 3 DT n 2 4 DG n 2 5 DG n 2 6 DC n 2 7 DG n 2 8 DC n 2 9 DC n 2 10 DG n 2 11 DG n 2 12 DT n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _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 1 1 sample ? ? 'synthetic construct' ? 32630 ? 2 1 sample ? ? 'synthetic construct' ? 32630 ? # 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 # 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 DA 1 1 1 DA A A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DG 5 5 5 DG G A . n A 1 6 DC 6 6 6 DC C A . n A 1 7 DG 7 7 7 DG G A . n A 1 8 DC 8 8 8 DC C A . n A 1 9 DC 9 9 9 DC C A . n A 1 10 DA 10 10 10 DA A A . n A 1 11 DC 11 11 11 DC C A . n A 1 12 DA 12 12 12 DA A A . n B 2 1 DT 1 13 13 DT T B . n B 2 2 DG 2 14 14 DG G B . n B 2 3 DT 3 15 15 DT T B . n B 2 4 DG 4 16 16 DG G B . n B 2 5 DG 5 17 17 DG G B . n B 2 6 DC 6 18 18 DC C B . n B 2 7 DG 7 19 19 DG G B . n B 2 8 DC 8 20 20 DC C B . n B 2 9 DC 9 21 21 DC C B . n B 2 10 DG 10 22 22 DG G B . n B 2 11 DG 11 23 23 DG G B . n B 2 12 DT 12 24 24 DT T B . n # _software.name NUCLSQ _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 1 # _cell.entry_id 1VTD _cell.length_a 65.900 _cell.length_b 65.900 _cell.length_c 47.100 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 9 _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 1VTD _symmetry.space_group_name_H-M 'H 3' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1VTD _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 54.21 _exptl_crystal.density_Matthews 2.69 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.temp 277.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.10 _exptl_crystal_grow.pdbx_details 'pH 6.10, VAPOR DIFFUSION, temperature 277.00K' _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 WATER 1 2 3 1 2 1 CACODYLATE 4 5 6 1 3 1 SPERMINE 7 8 9 1 4 1 'MG ACETATE' 10 11 12 1 5 2 WATER 13 14 15 1 6 2 MPD 16 17 18 # _diffrn.id 1 _diffrn.ambient_temp 273.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector DIFFRACTOMETER _diffrn_detector.type NICOLET _diffrn_detector.pdbx_collection_date ? _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 . _diffrn_radiation_wavelength.wt 1.0 # _reflns.entry_id 1VTD _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F 1.000 _reflns.d_resolution_low 10 _reflns.d_resolution_high 2.8 _reflns.number_obs 1584 _reflns.number_all ? _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_CC_half ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_Rrim_I_all ? # _refine.entry_id 1VTD _refine.ls_number_reflns_obs 1101 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I 3.000 _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.000 _refine.ls_d_res_high 2.800 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.1530000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _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 ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _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_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _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_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_phase_error ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _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_ESU_R ? _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 486 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 486 _refine_hist.d_res_high 2.800 _refine_hist.d_res_low 10.000 # _database_PDB_matrix.entry_id 1VTD _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 # _struct.entry_id 1VTD _struct.title 'UNUSUAL HELICAL PACKING IN CRYSTALS OF DNA BEARING A MUTATION HOT SPOT' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1VTD _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'B-DNA, DOUBLE HELIX, 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 2 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 PDB 1VTD 1VTD 1 ? ? ? 2 PDB 1VTD 1VTD 2 ? ? ? # 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 1VTD A 1 ? 12 ? 1VTD 1 ? 12 ? 1 12 2 2 1VTD B 1 ? 12 ? 1VTD 13 ? 24 ? 13 24 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details 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)' 1050 ? 1 MORE -6 ? 1 'SSA (A^2)' 4650 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _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_ _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 hydrog1 hydrog ? ? A DA 1 N1 ? ? ? 1_555 B DG 11 N1 ? ? A DA 1 B DG 23 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog2 hydrog ? ? A DA 1 N6 ? ? ? 1_555 B DG 11 O6 ? ? A DA 1 B DG 23 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog3 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 2 B DG 22 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog4 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 11 N2 ? ? A DC 2 B DG 23 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog5 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 4 B DC 20 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog6 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog7 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B DC 8 O2 ? ? A DG 5 B DC 20 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog8 hydrog ? ? A DC 6 O2 ? ? ? 1_555 B DG 7 N2 ? ? A DC 6 B DG 19 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog9 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B DG 5 O6 ? ? A DG 7 B DG 17 1_555 ? ? ? ? ? ? 'DG-DG MISPAIR' ? ? ? hydrog10 hydrog ? ? A DG 7 N2 ? ? ? 1_555 B DC 6 O2 ? ? A DG 7 B DC 18 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog11 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 8 B DG 16 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog12 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 5 N2 ? ? A DC 8 B DG 17 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog13 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DT 3 N3 ? ? A DC 9 B DT 15 1_555 ? ? ? ? ? ? TYPE_18_PAIR ? ? ? hydrog14 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DT 3 O4 ? ? A DC 9 B DT 15 1_555 ? ? ? ? ? ? TYPE_18_PAIR ? ? ? hydrog15 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 4 N1 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog16 hydrog ? ? A DA 10 N1 ? ? ? 1_555 B DG 2 N1 ? ? A DA 10 B DG 14 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog17 hydrog ? ? A DA 10 N6 ? ? ? 1_555 B DG 2 O6 ? ? A DA 10 B DG 14 1_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog18 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DT 1 O4 ? ? A DC 11 B DT 13 1_555 ? ? ? ? ? ? 'DC-DT MISPAIR' ? ? ? hydrog19 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O3'" A DG 4 ? ? P A DG 5 ? ? 1.520 1.607 -0.087 0.012 Y 2 1 "O3'" A DC 9 ? ? P A DA 10 ? ? 1.534 1.607 -0.073 0.012 Y 3 1 P A DA 10 ? ? "O5'" A DA 10 ? ? 1.669 1.593 0.076 0.010 N 4 1 "O3'" B DT 15 ? ? P B DG 16 ? ? 1.520 1.607 -0.087 0.012 Y 5 1 "O3'" B DG 16 ? ? "C3'" B DG 16 ? ? 1.334 1.419 -0.085 0.006 N 6 1 C2 B DC 20 ? ? N3 B DC 20 ? ? 1.408 1.353 0.055 0.008 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 DA 1 ? ? "C4'" A DA 1 ? ? "C3'" A DA 1 ? ? 99.82 104.50 -4.68 0.40 N 2 1 "C5'" A DA 1 ? ? "C4'" A DA 1 ? ? "O4'" A DA 1 ? ? 116.52 109.80 6.72 1.10 N 3 1 "C4'" A DA 1 ? ? "C3'" A DA 1 ? ? "C2'" A DA 1 ? ? 97.01 102.20 -5.19 0.70 N 4 1 "O4'" A DA 1 ? ? "C1'" A DA 1 ? ? N9 A DA 1 ? ? 101.88 108.00 -6.12 0.70 N 5 1 C5 A DA 1 ? ? C6 A DA 1 ? ? N1 A DA 1 ? ? 114.44 117.70 -3.26 0.50 N 6 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 102.03 108.00 -5.97 0.70 N 7 1 "C3'" A DC 3 ? ? "O3'" A DC 3 ? ? P A DG 4 ? ? 130.15 119.70 10.45 1.20 Y 8 1 "O3'" A DC 3 ? ? P A DG 4 ? ? OP2 A DG 4 ? ? 117.22 110.50 6.72 1.10 Y 9 1 OP1 A DG 4 ? ? P A DG 4 ? ? OP2 A DG 4 ? ? 110.21 119.60 -9.39 1.50 N 10 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 115.53 108.30 7.23 0.30 N 11 1 C6 A DG 4 ? ? N1 A DG 4 ? ? C2 A DG 4 ? ? 116.81 125.10 -8.29 0.60 N 12 1 N1 A DG 4 ? ? C2 A DG 4 ? ? N3 A DG 4 ? ? 128.79 123.90 4.89 0.60 N 13 1 C5 A DG 4 ? ? C6 A DG 4 ? ? N1 A DG 4 ? ? 116.82 111.50 5.32 0.50 N 14 1 C5 A DG 4 ? ? C6 A DG 4 ? ? O6 A DG 4 ? ? 122.26 128.60 -6.34 0.60 N 15 1 "C3'" A DG 4 ? ? "O3'" A DG 4 ? ? P A DG 5 ? ? 136.68 119.70 16.98 1.20 Y 16 1 OP1 A DG 5 ? ? P A DG 5 ? ? OP2 A DG 5 ? ? 109.49 119.60 -10.11 1.50 N 17 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 114.99 108.30 6.69 0.30 N 18 1 C6 A DG 5 ? ? N1 A DG 5 ? ? C2 A DG 5 ? ? 120.96 125.10 -4.14 0.60 N 19 1 C5 A DG 5 ? ? C6 A DG 5 ? ? N1 A DG 5 ? ? 115.25 111.50 3.75 0.50 N 20 1 "C3'" A DG 5 ? ? "O3'" A DG 5 ? ? P A DC 6 ? ? 132.59 119.70 12.89 1.20 Y 21 1 "O3'" A DG 5 ? ? P A DC 6 ? ? OP2 A DC 6 ? ? 117.84 110.50 7.34 1.10 Y 22 1 OP1 A DC 6 ? ? P A DC 6 ? ? OP2 A DC 6 ? ? 109.32 119.60 -10.28 1.50 N 23 1 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 113.64 108.30 5.34 0.30 N 24 1 "O3'" A DG 7 ? ? P A DC 8 ? ? "O5'" A DC 8 ? ? 91.29 104.00 -12.71 1.90 Y 25 1 "O3'" A DG 7 ? ? P A DC 8 ? ? OP2 A DC 8 ? ? 117.70 110.50 7.20 1.10 Y 26 1 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 114.06 108.30 5.76 0.30 N 27 1 N3 A DC 8 ? ? C4 A DC 8 ? ? C5 A DC 8 ? ? 119.49 121.90 -2.41 0.40 N 28 1 N3 A DC 9 ? ? C4 A DC 9 ? ? N4 A DC 9 ? ? 124.74 118.00 6.74 0.70 N 29 1 C5 A DC 9 ? ? C4 A DC 9 ? ? N4 A DC 9 ? ? 113.75 120.20 -6.45 0.70 N 30 1 "C3'" A DC 9 ? ? "O3'" A DC 9 ? ? P A DA 10 ? ? 149.45 119.70 29.75 1.20 Y 31 1 P A DA 10 ? ? "O5'" A DA 10 ? ? "C5'" A DA 10 ? ? 109.76 120.90 -11.14 1.60 N 32 1 N9 A DA 10 ? ? "C1'" A DA 10 ? ? "C2'" A DA 10 ? ? 100.50 112.60 -12.10 1.90 N 33 1 N1 A DA 10 ? ? C6 A DA 10 ? ? N6 A DA 10 ? ? 122.36 118.60 3.76 0.60 N 34 1 "C3'" A DA 10 ? ? "O3'" A DA 10 ? ? P A DC 11 ? ? 109.92 119.70 -9.78 1.20 Y 35 1 "O5'" A DC 11 ? ? P A DC 11 ? ? OP1 A DC 11 ? ? 119.95 110.70 9.25 1.20 N 36 1 "O4'" A DC 11 ? ? "C4'" A DC 11 ? ? "C3'" A DC 11 ? ? 101.92 104.50 -2.58 0.40 N 37 1 "O4'" A DC 11 ? ? "C1'" A DC 11 ? ? N1 A DC 11 ? ? 120.33 108.30 12.03 0.30 N 38 1 N3 A DC 11 ? ? C4 A DC 11 ? ? C5 A DC 11 ? ? 119.45 121.90 -2.45 0.40 N 39 1 "O4'" A DA 12 ? ? "C1'" A DA 12 ? ? N9 A DA 12 ? ? 111.72 108.30 3.42 0.30 N 40 1 C5 A DA 12 ? ? C6 A DA 12 ? ? N1 A DA 12 ? ? 114.61 117.70 -3.09 0.50 N 41 1 C2 B DT 13 ? ? N3 B DT 13 ? ? C4 B DT 13 ? ? 122.33 127.20 -4.87 0.60 N 42 1 N3 B DT 13 ? ? C4 B DT 13 ? ? C5 B DT 13 ? ? 118.94 115.20 3.74 0.60 N 43 1 "O4'" B DG 14 ? ? "C1'" B DG 14 ? ? N9 B DG 14 ? ? 114.72 108.30 6.42 0.30 N 44 1 C5 B DG 14 ? ? C6 B DG 14 ? ? N1 B DG 14 ? ? 114.90 111.50 3.40 0.50 N 45 1 "C3'" B DG 14 ? ? "O3'" B DG 14 ? ? P B DT 15 ? ? 111.05 119.70 -8.65 1.20 Y 46 1 "O5'" B DT 15 ? ? P B DT 15 ? ? OP1 B DT 15 ? ? 120.37 110.70 9.67 1.20 N 47 1 "O4'" B DT 15 ? ? "C1'" B DT 15 ? ? N1 B DT 15 ? ? 110.15 108.30 1.85 0.30 N 48 1 N1 B DT 15 ? ? C2 B DT 15 ? ? N3 B DT 15 ? ? 119.98 114.60 5.38 0.60 N 49 1 C2 B DT 15 ? ? N3 B DT 15 ? ? C4 B DT 15 ? ? 119.18 127.20 -8.02 0.60 N 50 1 N3 B DT 15 ? ? C4 B DT 15 ? ? C5 B DT 15 ? ? 121.08 115.20 5.88 0.60 N 51 1 C5 B DT 15 ? ? C4 B DT 15 ? ? O4 B DT 15 ? ? 120.13 124.90 -4.77 0.70 N 52 1 "C3'" B DT 15 ? ? "O3'" B DT 15 ? ? P B DG 16 ? ? 147.19 119.70 27.49 1.20 Y 53 1 "O3'" B DT 15 ? ? P B DG 16 ? ? OP2 B DG 16 ? ? 118.26 110.50 7.76 1.10 Y 54 1 OP1 B DG 16 ? ? P B DG 16 ? ? OP2 B DG 16 ? ? 109.36 119.60 -10.24 1.50 N 55 1 "C4'" B DG 16 ? ? "C3'" B DG 16 ? ? "O3'" B DG 16 ? ? 126.32 112.30 14.02 2.00 N 56 1 "C5'" B DG 17 ? ? "C4'" B DG 17 ? ? "O4'" B DG 17 ? ? 142.05 109.80 32.25 1.10 N 57 1 P B DC 18 ? ? "O5'" B DC 18 ? ? "C5'" B DC 18 ? ? 110.91 120.90 -9.99 1.60 N 58 1 "O4'" B DC 18 ? ? "C1'" B DC 18 ? ? N1 B DC 18 ? ? 110.47 108.30 2.17 0.30 N 59 1 "C1'" B DC 20 ? ? "O4'" B DC 20 ? ? "C4'" B DC 20 ? ? 116.44 110.30 6.14 0.70 N 60 1 "O4'" B DC 20 ? ? "C1'" B DC 20 ? ? N1 B DC 20 ? ? 120.78 108.30 12.48 0.30 N 61 1 "C3'" B DC 20 ? ? "O3'" B DC 20 ? ? P B DC 21 ? ? 135.62 119.70 15.92 1.20 Y 62 1 OP1 B DC 21 ? ? P B DC 21 ? ? OP2 B DC 21 ? ? 109.99 119.60 -9.61 1.50 N 63 1 "O4'" B DC 21 ? ? "C1'" B DC 21 ? ? N1 B DC 21 ? ? 117.07 108.30 8.77 0.30 N 64 1 "O4'" B DG 22 ? ? "C4'" B DG 22 ? ? "C3'" B DG 22 ? ? 101.15 104.50 -3.35 0.40 N 65 1 "O4'" B DG 22 ? ? "C1'" B DG 22 ? ? N9 B DG 22 ? ? 110.98 108.30 2.68 0.30 N 66 1 C5 B DG 22 ? ? C6 B DG 22 ? ? N1 B DG 22 ? ? 114.87 111.50 3.37 0.50 N 67 1 "O5'" B DG 23 ? ? P B DG 23 ? ? OP1 B DG 23 ? ? 121.84 110.70 11.14 1.20 N 68 1 P B DG 23 ? ? "O5'" B DG 23 ? ? "C5'" B DG 23 ? ? 132.35 120.90 11.45 1.60 N 69 1 "O4'" B DT 24 ? ? "C1'" B DT 24 ? ? N1 B DT 24 ? ? 111.87 108.30 3.57 0.30 N 70 1 C2 B DT 24 ? ? N3 B DT 24 ? ? C4 B DT 24 ? ? 122.81 127.20 -4.39 0.60 N 71 1 N3 B DT 24 ? ? C4 B DT 24 ? ? C5 B DT 24 ? ? 118.96 115.20 3.76 0.60 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 # 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 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1VTD 'double helix' 1VTD 'b-form double helix' 1VTD 'mismatched base pair' 1VTD 'triple 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 DA 1 1_555 B DG 11 1_555 0.655 1.498 -0.498 -3.336 -6.297 -16.178 1 A_DA1:DG23_B A 1 ? B 23 ? 8 1 1 A DC 2 1_555 B DG 10 1_555 -1.156 4.460 -1.006 -18.534 -27.855 -102.516 2 A_DC2:DG22_B A 2 ? B 22 ? ? ? 1 A DG 4 1_555 B DC 9 1_555 0.654 0.646 1.065 -9.255 -19.540 21.284 3 A_DG4:DC21_B A 4 ? B 21 ? ? 1 1 A DG 5 1_555 B DC 8 1_555 -1.480 -0.038 0.910 -1.540 -27.184 6.864 4 A_DG5:DC20_B A 5 ? B 20 ? ? 1 1 A DC 6 1_555 B DG 7 1_555 -1.476 0.358 0.013 6.614 -17.665 1.276 5 A_DC6:DG19_B A 6 ? B 19 ? ? 1 1 A DG 7 1_555 B DC 6 1_555 0.626 0.812 1.613 0.584 -24.890 14.113 6 A_DG7:DC18_B A 7 ? B 18 ? ? 1 1 A DC 8 1_555 B DG 4 1_555 0.075 0.782 -1.575 -6.958 -17.476 -28.763 7 A_DC8:DG16_B A 8 ? B 16 ? ? ? 1 A DC 9 1_555 B DT 3 1_555 0.789 -1.873 -0.787 -4.766 -24.836 3.174 8 A_DC9:DT15_B A 9 ? B 15 ? 18 1 1 A DA 10 1_555 B DG 2 1_555 0.152 1.098 -1.647 -1.937 -17.769 -12.665 9 A_DA10:DG14_B A 10 ? B 14 ? 8 1 1 A DC 11 1_555 B DT 1 1_555 0.552 0.964 -1.111 -21.663 -15.214 -52.646 10 A_DC11:DT13_B A 11 ? B 13 ? ? ? # 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 DA 1 1_555 B DG 11 1_555 A DC 2 1_555 B DG 10 1_555 0.596 -1.097 2.511 -0.675 -11.236 74.798 -0.629 -0.502 2.626 -9.200 0.553 75.518 1 AA_DA1DC2:DG22DG23_BB A 1 ? B 23 ? A 2 ? B 22 ? 1 A DC 2 1_555 B DG 10 1_555 A DG 4 1_555 B DC 9 1_555 0.632 3.051 5.869 3.859 -0.086 17.073 10.123 2.191 5.850 -0.285 -12.786 17.501 2 AA_DC2DG4:DC21DG22_BB A 2 ? B 22 ? A 4 ? B 21 ? 1 A DG 4 1_555 B DC 9 1_555 A DG 5 1_555 B DC 8 1_555 -1.720 0.372 2.781 -9.136 10.135 21.670 -1.982 1.343 3.116 24.121 21.743 25.564 3 AA_DG4DG5:DC20DC21_BB A 4 ? B 21 ? A 5 ? B 20 ? 1 A DG 5 1_555 B DC 8 1_555 A DC 6 1_555 B DG 7 1_555 -0.400 0.614 3.336 4.590 -10.623 37.195 2.201 1.154 2.988 -16.181 -6.992 38.892 4 AA_DG5DC6:DG19DC20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DC 6 1_555 B DG 7 1_555 A DG 7 1_555 B DC 6 1_555 0.973 1.453 3.937 -4.003 6.698 46.416 1.147 -1.621 4.005 8.428 5.037 47.032 5 AA_DC6DG7:DC18DG19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A DG 7 1_555 B DC 6 1_555 A DC 8 1_555 B DG 4 1_555 -1.038 -0.116 5.328 -7.483 -3.195 49.332 0.246 0.331 5.418 -3.797 8.896 49.957 6 AA_DG7DC8:DG16DC18_BB A 7 ? B 18 ? A 8 ? B 16 ? 1 A DC 8 1_555 B DG 4 1_555 A DC 9 1_555 B DT 3 1_555 1.870 0.671 3.506 1.229 -3.605 37.473 1.540 -2.726 3.486 -5.593 -1.907 37.659 7 AA_DC8DC9:DT15DG16_BB A 8 ? B 16 ? A 9 ? B 15 ? 1 A DC 9 1_555 B DT 3 1_555 A DA 10 1_555 B DG 2 1_555 -1.503 0.675 3.315 0.023 2.363 35.708 0.751 2.450 3.351 3.848 -0.038 35.784 8 AA_DC9DA10:DG14DT15_BB A 9 ? B 15 ? A 10 ? B 14 ? 1 A DA 10 1_555 B DG 2 1_555 A DC 11 1_555 B DT 1 1_555 -1.246 -0.894 3.736 -7.104 -6.357 31.509 -0.262 0.730 4.014 -11.384 12.722 32.884 9 AA_DA10DC11:DT13DG14_BB A 10 ? B 14 ? A 11 ? B 13 ? # _atom_sites.entry_id 1VTD _atom_sites.fract_transf_matrix[1][1] 0.015175 _atom_sites.fract_transf_matrix[1][2] 0.008761 _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] 0.017522 _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] 0.021231 _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 # loop_