data_1QYL # _entry.id 1QYL # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 1QYL pdb_00001qyl 10.2210/pdb1qyl/pdb NDB UD0041 ? ? RCSB RCSB020227 ? ? WWPDB D_1000020227 ? ? # 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 2003-10-21 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-14 5 'Structure model' 1 4 2024-04-03 # _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' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 5 '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 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' diffrn_source 5 4 'Structure model' pdbx_struct_conn_angle 6 4 'Structure model' struct_conn 7 4 'Structure model' struct_site 8 5 'Structure model' pdbx_initial_refinement_model # 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' '_diffrn_source.pdbx_synchrotron_site' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 8 4 'Structure model' '_pdbx_struct_conn_angle.value' 9 4 'Structure model' '_struct_conn.pdbx_dist_value' 10 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 11 4 'Structure model' '_struct_conn.ptnr2_symmetry' 12 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 13 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 14 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1QYL _pdbx_database_status.recvd_initial_deposition_date 2003-09-11 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _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 1QYK 'GCATGCT + Barium' unspecified PDB 1QZL 'GCATGCT + Cobalt' unspecified PDB 1R2O 'GCATGCT + Ni2+' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Cardin, C.J.' 1 'Gan, Y.' 2 'Thorpe, J.H.' 3 'Teixeira, S.C.M.' 4 'Gale, B.C.' 5 'Moraes, M.I.A.' 6 # _citation.id primary _citation.title 'Metal Ion Distribution and Stabilisation of the DNA Quadruplex Structure Formed by d(GCATGCT)' _citation.journal_abbrev 'To be Published' _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 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Cardin, C.J.' 1 ? primary 'GAN, Y.' 2 ? primary 'Thorpe, J.H.' 3 ? primary 'Teixeira, S.C.M.' 4 ? primary 'Gale, B.C.' 5 ? primary 'Moraes, M.I.A.' 6 ? # 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*AP*TP*GP*CP*T)-3'" 2113.410 1 ? ? ? ? 2 non-polymer syn 'VANADIUM ION' 50.941 1 ? ? ? ? 3 water nat water 18.015 45 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DG)(DC)(DA)(DT)(DG)(DC)(DT)' _entity_poly.pdbx_seq_one_letter_code_can GCATGCT _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'VANADIUM ION' V 3 water 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 DC n 1 3 DA n 1 4 DT n 1 5 DG n 1 6 DC n 1 7 DT n # 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 V non-polymer . 'VANADIUM ION' ? 'V 3' 50.941 # 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 G A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DA 3 3 3 DA A A . n A 1 4 DT 4 4 4 DT T 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 DT 7 7 7 DT T A . 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 B 2 V 1 8 1 V V A . C 3 HOH 1 100 100 HOH HOH A . C 3 HOH 2 101 101 HOH HOH A . C 3 HOH 3 102 102 HOH HOH A . C 3 HOH 4 103 103 HOH HOH A . C 3 HOH 5 104 104 HOH HOH A . C 3 HOH 6 105 105 HOH HOH A . C 3 HOH 7 106 106 HOH HOH A . C 3 HOH 8 107 107 HOH HOH A . C 3 HOH 9 108 108 HOH HOH A . C 3 HOH 10 109 109 HOH HOH A . C 3 HOH 11 110 110 HOH HOH A . C 3 HOH 12 111 111 HOH HOH A . C 3 HOH 13 112 112 HOH HOH A . C 3 HOH 14 113 113 HOH HOH A . C 3 HOH 15 114 114 HOH HOH A . C 3 HOH 16 115 115 HOH HOH A . C 3 HOH 17 116 116 HOH HOH A . C 3 HOH 18 117 117 HOH HOH A . C 3 HOH 19 118 118 HOH HOH A . C 3 HOH 20 119 119 HOH HOH A . C 3 HOH 21 120 120 HOH HOH A . C 3 HOH 22 121 121 HOH HOH A . C 3 HOH 23 122 122 HOH HOH A . C 3 HOH 24 123 123 HOH HOH A . C 3 HOH 25 124 124 HOH HOH A . C 3 HOH 26 125 125 HOH HOH A . C 3 HOH 27 126 126 HOH HOH A . C 3 HOH 28 127 127 HOH HOH A . C 3 HOH 29 128 128 HOH HOH A . C 3 HOH 30 129 129 HOH HOH A . C 3 HOH 31 130 130 HOH HOH A . C 3 HOH 32 131 131 HOH HOH A . C 3 HOH 33 132 132 HOH HOH A . C 3 HOH 34 133 133 HOH HOH A . C 3 HOH 35 134 134 HOH HOH A . C 3 HOH 36 135 135 HOH HOH A . C 3 HOH 37 136 136 HOH HOH A . C 3 HOH 38 137 137 HOH HOH A . C 3 HOH 39 138 138 HOH HOH A . C 3 HOH 40 139 139 HOH HOH A . C 3 HOH 41 140 140 HOH HOH A . C 3 HOH 42 141 141 HOH HOH A . C 3 HOH 43 142 142 HOH HOH A . C 3 HOH 44 143 143 HOH HOH A . C 3 HOH 45 144 144 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHELX 'model building' . ? 1 SHELXL-97 refinement . ? 2 XDS 'data reduction' . ? 3 XDS 'data scaling' . ? 4 XTALVIEW refinement . ? 5 # _cell.entry_id 1QYL _cell.length_a 22.532 _cell.length_b 58.469 _cell.length_c 24.148 _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 1QYL _symmetry.space_group_name_H-M 'C 2 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 21 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1QYL _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.81 _exptl_crystal.density_percent_sol 32.16 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 290 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 5.7 _exptl_crystal_grow.pdbx_details 'NaCacodylate, Vanadium Chloride, Sodium Chloride, MPD, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 290K' _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 NaCacodylate ? ? ? 1 2 1 'Vanadium Chloride' ? ? ? 1 3 1 'Sodium Chloride' ? ? ? 1 4 1 MPD ? ? ? 1 5 1 H2O ? ? ? 1 6 2 NaCacodylate ? ? ? 1 7 2 'Vanadium Chloride' ? ? ? 1 8 2 MPD ? ? ? 1 9 2 H2O ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2003-08-19 _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 0.8416 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'EMBL/DESY, HAMBURG BEAMLINE BW7B' _diffrn_source.pdbx_synchrotron_site 'EMBL/DESY, HAMBURG' _diffrn_source.pdbx_synchrotron_beamline BW7B _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.8416 # _reflns.entry_id 1QYL _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 5.8 _reflns.d_resolution_high 1.0 _reflns.number_obs 8848 _reflns.number_all ? _reflns.percent_possible_obs 98.4 _reflns.pdbx_Rmerge_I_obs 0.095 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 20.1 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.00 _reflns_shell.d_res_low 1.20 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.147 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 12.63 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 3718 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 1QYL _refine.ls_number_reflns_obs 8406 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _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 5.80 _refine.ls_d_res_high 1.00 _refine.ls_percent_reflns_obs 98.4 _refine.ls_R_factor_obs 0.1493 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1493 _refine.ls_R_factor_R_free 0.1838 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 3.7 _refine.ls_number_reflns_R_free 311 _refine.ls_number_parameters 1655 _refine.ls_number_restraints 1425 _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 'FREE R' _refine.details 'ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)' _refine.pdbx_starting_model 'NDB entry udg028' _refine.pdbx_method_to_determine_struct 'AB INITIO' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'ENGH AND HUBER' _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.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_phase_error ? _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_analyze.entry_id 1QYL _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues 0 _refine_analyze.occupancy_sum_hydrogen 0.00 _refine_analyze.occupancy_sum_non_hydrogen 180.50 _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _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 140 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 45 _refine_hist.number_atoms_total 186 _refine_hist.d_res_high 1.00 _refine_hist.d_res_low 5.80 # 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 0.023 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.042 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes 0.0036 ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr 0.013 ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt 0.033 ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps 0.000 ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 1QYL _pdbx_refine.R_factor_all_no_cutoff 0.1493 _pdbx_refine.R_factor_obs_no_cutoff ? _pdbx_refine.free_R_factor_no_cutoff 0.1838 _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 3.7 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 311 _pdbx_refine.R_factor_all_4sig_cutoff 0.1488 _pdbx_refine.R_factor_obs_4sig_cutoff ? _pdbx_refine.free_R_factor_4sig_cutoff 0.1814 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 3.2 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 266 _pdbx_refine.number_reflns_obs_4sig_cutoff 8224 _pdbx_refine.number_reflns_obs_no_cutoff ? _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _database_PDB_matrix.entry_id 1QYL _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] 0.000000 _database_PDB_matrix.origx_vector[2] 0.000000 _database_PDB_matrix.origx_vector[3] 0.000000 # _struct.entry_id 1QYL _struct.title 'GCATGCT + Vanadium' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1QYL _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Quadruplex DNA, 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 ? C N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1QYL _struct_ref.pdbx_db_accession 1QYL _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1QYL _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 7 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1QYL _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 7 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 7 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 _pdbx_struct_assembly_gen.asym_id_list A,B,C # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_655 -x+1,-y,z -1.0000000000 0.0000000000 0.0000000000 22.5320000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 3_655 -x+1,y,-z -1.0000000000 0.0000000000 0.0000000000 22.5320000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 4 'crystal symmetry operation' 4_555 x,-y,-z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _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 metalc1 metalc ? ? B V . V ? ? ? 1_555 C HOH . O ? ? A V 8 A HOH 103 1_555 ? ? ? ? ? ? ? 2.226 ? ? metalc2 metalc ? ? B V . V ? ? ? 1_555 C HOH . O ? ? A V 8 A HOH 103 3_555 ? ? ? ? ? ? ? 2.226 ? ? metalc3 metalc ? ? B V . V ? ? ? 1_555 C HOH . O ? ? A V 8 A HOH 103 4_555 ? ? ? ? ? ? ? 2.226 ? ? metalc4 metalc ? ? B V . V ? ? ? 1_555 C HOH . O ? ? A V 8 A HOH 103 2_555 ? ? ? ? ? ? ? 2.226 ? ? metalc5 metalc ? ? B V . V ? ? ? 1_555 C HOH . O ? ? A V 8 A HOH 108 1_555 ? ? ? ? ? ? ? 2.100 ? ? metalc6 metalc ? ? B V . V ? ? ? 1_555 C HOH . O ? ? A V 8 A HOH 108 3_555 ? ? ? ? ? ? ? 2.100 ? ? metalc7 metalc ? ? B V . V ? ? ? 1_555 C HOH . O ? ? A V 8 A HOH 108 4_555 ? ? ? ? ? ? ? 2.100 ? ? metalc8 metalc ? ? B V . V ? ? ? 1_555 C HOH . O ? ? A V 8 A HOH 108 2_555 ? ? ? ? ? ? ? 2.100 ? ? metalc9 metalc ? ? B V . V ? ? ? 1_555 C HOH . O ? ? A V 8 A HOH 124 1_555 ? ? ? ? ? ? ? 2.115 ? ? metalc10 metalc ? ? B V . V ? ? ? 1_555 C HOH . O ? ? A V 8 A HOH 124 2_555 ? ? ? ? ? ? ? 2.115 ? ? metalc11 metalc ? ? B V . V ? ? ? 1_555 C HOH . O ? ? A V 8 A HOH 124 3_555 ? ? ? ? ? ? ? 2.115 ? ? metalc12 metalc ? ? B V . V ? ? ? 1_555 C HOH . O ? ? A V 8 A HOH 124 4_555 ? ? ? ? ? ? ? 2.115 ? ? hydrog1 hydrog ? ? A DG 1 N2 ? ? ? 1_555 A DC 6 O2 ? ? A DG 1 A DC 6 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog2 hydrog ? ? A DC 2 O2 ? ? ? 1_555 A DG 5 N2 ? ? A DC 2 A DG 5 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? C HOH . ? A HOH 103 ? 1_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 103 ? 3_555 180.0 ? 2 O ? C HOH . ? A HOH 103 ? 1_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 103 ? 4_555 180.0 ? 3 O ? C HOH . ? A HOH 103 ? 3_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 103 ? 4_555 0.0 ? 4 O ? C HOH . ? A HOH 103 ? 1_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 103 ? 2_555 0.0 ? 5 O ? C HOH . ? A HOH 103 ? 3_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 103 ? 2_555 180.0 ? 6 O ? C HOH . ? A HOH 103 ? 4_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 103 ? 2_555 180.0 ? 7 O ? C HOH . ? A HOH 103 ? 1_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 1_555 75.5 ? 8 O ? C HOH . ? A HOH 103 ? 3_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 1_555 104.5 ? 9 O ? C HOH . ? A HOH 103 ? 4_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 1_555 104.5 ? 10 O ? C HOH . ? A HOH 103 ? 2_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 1_555 75.5 ? 11 O ? C HOH . ? A HOH 103 ? 1_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 3_555 104.5 ? 12 O ? C HOH . ? A HOH 103 ? 3_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 3_555 75.5 ? 13 O ? C HOH . ? A HOH 103 ? 4_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 3_555 75.5 ? 14 O ? C HOH . ? A HOH 103 ? 2_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 3_555 104.5 ? 15 O ? C HOH . ? A HOH 108 ? 1_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 3_555 29.5 ? 16 O ? C HOH . ? A HOH 103 ? 1_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 4_555 104.5 ? 17 O ? C HOH . ? A HOH 103 ? 3_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 4_555 75.5 ? 18 O ? C HOH . ? A HOH 103 ? 4_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 4_555 75.5 ? 19 O ? C HOH . ? A HOH 103 ? 2_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 4_555 104.5 ? 20 O ? C HOH . ? A HOH 108 ? 1_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 4_555 174.3 ? 21 O ? C HOH . ? A HOH 108 ? 3_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 4_555 151.1 ? 22 O ? C HOH . ? A HOH 103 ? 1_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 2_555 75.5 ? 23 O ? C HOH . ? A HOH 103 ? 3_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 2_555 104.5 ? 24 O ? C HOH . ? A HOH 103 ? 4_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 2_555 104.5 ? 25 O ? C HOH . ? A HOH 103 ? 2_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 2_555 75.5 ? 26 O ? C HOH . ? A HOH 108 ? 1_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 2_555 151.1 ? 27 O ? C HOH . ? A HOH 108 ? 3_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 2_555 174.3 ? 28 O ? C HOH . ? A HOH 108 ? 4_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 108 ? 2_555 29.5 ? 29 O ? C HOH . ? A HOH 103 ? 1_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 1_555 90.0 ? 30 O ? C HOH . ? A HOH 103 ? 3_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 1_555 90.0 ? 31 O ? C HOH . ? A HOH 103 ? 4_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 1_555 90.0 ? 32 O ? C HOH . ? A HOH 103 ? 2_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 1_555 90.0 ? 33 O ? C HOH . ? A HOH 108 ? 1_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 1_555 87.1 ? 34 O ? C HOH . ? A HOH 108 ? 3_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 1_555 92.9 ? 35 O ? C HOH . ? A HOH 108 ? 4_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 1_555 87.1 ? 36 O ? C HOH . ? A HOH 108 ? 2_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 1_555 92.9 ? 37 O ? C HOH . ? A HOH 103 ? 1_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 2_555 90.0 ? 38 O ? C HOH . ? A HOH 103 ? 3_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 2_555 90.0 ? 39 O ? C HOH . ? A HOH 103 ? 4_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 2_555 90.0 ? 40 O ? C HOH . ? A HOH 103 ? 2_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 2_555 90.0 ? 41 O ? C HOH . ? A HOH 108 ? 1_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 2_555 92.9 ? 42 O ? C HOH . ? A HOH 108 ? 3_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 2_555 87.1 ? 43 O ? C HOH . ? A HOH 108 ? 4_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 2_555 92.9 ? 44 O ? C HOH . ? A HOH 108 ? 2_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 2_555 87.1 ? 45 O ? C HOH . ? A HOH 124 ? 1_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 2_555 180.0 ? 46 O ? C HOH . ? A HOH 103 ? 1_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 3_555 90.0 ? 47 O ? C HOH . ? A HOH 103 ? 3_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 3_555 90.0 ? 48 O ? C HOH . ? A HOH 103 ? 4_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 3_555 90.0 ? 49 O ? C HOH . ? A HOH 103 ? 2_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 3_555 90.0 ? 50 O ? C HOH . ? A HOH 108 ? 1_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 3_555 92.9 ? 51 O ? C HOH . ? A HOH 108 ? 3_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 3_555 87.1 ? 52 O ? C HOH . ? A HOH 108 ? 4_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 3_555 92.9 ? 53 O ? C HOH . ? A HOH 108 ? 2_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 3_555 87.1 ? 54 O ? C HOH . ? A HOH 124 ? 1_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 3_555 180.0 ? 55 O ? C HOH . ? A HOH 124 ? 2_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 3_555 0.0 ? 56 O ? C HOH . ? A HOH 103 ? 1_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 4_555 90.0 ? 57 O ? C HOH . ? A HOH 103 ? 3_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 4_555 90.0 ? 58 O ? C HOH . ? A HOH 103 ? 4_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 4_555 90.0 ? 59 O ? C HOH . ? A HOH 103 ? 2_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 4_555 90.0 ? 60 O ? C HOH . ? A HOH 108 ? 1_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 4_555 87.1 ? 61 O ? C HOH . ? A HOH 108 ? 3_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 4_555 92.9 ? 62 O ? C HOH . ? A HOH 108 ? 4_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 4_555 87.1 ? 63 O ? C HOH . ? A HOH 108 ? 2_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 4_555 92.9 ? 64 O ? C HOH . ? A HOH 124 ? 1_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 4_555 0.0 ? 65 O ? C HOH . ? A HOH 124 ? 2_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 4_555 180.0 ? 66 O ? C HOH . ? A HOH 124 ? 3_555 V ? B V . ? A V 8 ? 1_555 O ? C HOH . ? A HOH 124 ? 4_555 180.0 ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id V _struct_site.pdbx_auth_seq_id 8 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 12 _struct_site.details 'BINDING SITE FOR RESIDUE V A 8' # 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 12 HOH C . ? HOH A 103 . ? 3_555 ? 2 AC1 12 HOH C . ? HOH A 103 . ? 4_555 ? 3 AC1 12 HOH C . ? HOH A 103 . ? 1_555 ? 4 AC1 12 HOH C . ? HOH A 103 . ? 2_555 ? 5 AC1 12 HOH C . ? HOH A 108 . ? 3_555 ? 6 AC1 12 HOH C . ? HOH A 108 . ? 4_555 ? 7 AC1 12 HOH C . ? HOH A 108 . ? 1_555 ? 8 AC1 12 HOH C . ? HOH A 108 . ? 2_555 ? 9 AC1 12 HOH C . ? HOH A 124 . ? 3_555 ? 10 AC1 12 HOH C . ? HOH A 124 . ? 1_555 ? 11 AC1 12 HOH C . ? HOH A 124 . ? 4_555 ? 12 AC1 12 HOH C . ? HOH A 124 . ? 2_555 ? # 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 "O4'" A DG 1 ? ? "C1'" A DG 1 ? ? 1.504 1.420 0.084 0.011 N 2 1 C2 A DT 4 ? ? N3 A DT 4 ? ? 1.316 1.373 -0.057 0.008 N 3 1 N3 A DT 4 ? ? C4 A DT 4 ? ? 1.334 1.382 -0.048 0.008 N 4 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? 1.501 1.420 0.081 0.011 N 5 1 N7 A DG 5 ? ? C8 A DG 5 ? ? 1.267 1.305 -0.038 0.006 N 6 1 N1 A DC 6 ? ? C6 A DC 6 ? ? 1.328 1.367 -0.039 0.006 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 "O5'" A DG 1 ? ? "C5'" A DG 1 ? ? "C4'" A DG 1 ? ? 102.41 109.40 -6.99 0.80 N 2 1 "O4'" A DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 102.77 108.00 -5.23 0.70 N 3 1 N3 A DC 2 ? ? C4 A DC 2 ? ? C5 A DC 2 ? ? 124.41 121.90 2.51 0.40 N 4 1 C6 A DT 4 ? ? N1 A DT 4 ? ? C2 A DT 4 ? ? 117.33 121.30 -3.97 0.50 N 5 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 103.58 108.00 -4.42 0.70 N 6 1 "C1'" A DC 6 ? ? "O4'" A DC 6 ? ? "C4'" A DC 6 ? ? 103.80 110.10 -6.30 1.00 N 7 1 "O4'" A DC 6 ? ? "C1'" A DC 6 ? ? "C2'" A DC 6 ? ? 100.28 105.90 -5.62 0.80 N 8 1 N1 A DT 7 ? ? C2 A DT 7 ? ? N3 A DT 7 ? ? 119.18 114.60 4.58 0.60 N 9 1 C2 A DT 7 ? ? N3 A DT 7 ? ? C4 A DT 7 ? ? 122.09 127.20 -5.11 0.60 N 10 1 N1 A DT 7 ? ? C2 A DT 7 ? ? O2 A DT 7 ? ? 116.14 123.10 -6.96 0.80 N 11 1 N3 A DT 7 ? ? C4 A DT 7 ? ? O4 A DT 7 ? ? 116.14 119.90 -3.76 0.60 N 12 1 C4 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 130.99 119.00 11.99 0.60 N 13 1 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 109.15 122.90 -13.75 0.60 N # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A V 8 ? B V . 2 1 A HOH 100 ? C HOH . 3 1 A HOH 103 ? C HOH . 4 1 A HOH 119 ? C HOH . 5 1 A HOH 124 ? C HOH . # 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 V V V N N 147 # 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 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1QYL 'double helix' 1QYL 'hairpin loop' # 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 A DC 6 1_555 -3.276 8.562 -0.358 -3.418 40.132 177.203 1 A_DG1:DC6_A A 1 ? A 6 ? ? ? 1 A DC 2 1_555 A DG 5 1_555 3.359 8.461 -0.216 11.309 34.602 177.018 2 A_DC2:DG5_A A 2 ? A 5 ? ? ? # _ndb_struct_na_base_pair_step.model_number 1 _ndb_struct_na_base_pair_step.i_label_asym_id_1 A _ndb_struct_na_base_pair_step.i_label_comp_id_1 DG _ndb_struct_na_base_pair_step.i_label_seq_id_1 1 _ndb_struct_na_base_pair_step.i_symmetry_1 1_555 _ndb_struct_na_base_pair_step.j_label_asym_id_1 A _ndb_struct_na_base_pair_step.j_label_comp_id_1 DC _ndb_struct_na_base_pair_step.j_label_seq_id_1 6 _ndb_struct_na_base_pair_step.j_symmetry_1 1_555 _ndb_struct_na_base_pair_step.i_label_asym_id_2 A _ndb_struct_na_base_pair_step.i_label_comp_id_2 DC _ndb_struct_na_base_pair_step.i_label_seq_id_2 2 _ndb_struct_na_base_pair_step.i_symmetry_2 1_555 _ndb_struct_na_base_pair_step.j_label_asym_id_2 A _ndb_struct_na_base_pair_step.j_label_comp_id_2 DG _ndb_struct_na_base_pair_step.j_label_seq_id_2 5 _ndb_struct_na_base_pair_step.j_symmetry_2 1_555 _ndb_struct_na_base_pair_step.shift 0.290 _ndb_struct_na_base_pair_step.slide 0.422 _ndb_struct_na_base_pair_step.rise 2.889 _ndb_struct_na_base_pair_step.tilt -0.772 _ndb_struct_na_base_pair_step.roll 5.911 _ndb_struct_na_base_pair_step.twist 28.484 _ndb_struct_na_base_pair_step.x_displacement -0.319 _ndb_struct_na_base_pair_step.y_displacement -0.730 _ndb_struct_na_base_pair_step.helical_rise 2.907 _ndb_struct_na_base_pair_step.inclination 11.849 _ndb_struct_na_base_pair_step.tip 1.547 _ndb_struct_na_base_pair_step.helical_twist 29.088 _ndb_struct_na_base_pair_step.step_number 1 _ndb_struct_na_base_pair_step.step_name AA_DG1DC2:DG5DC6_AA _ndb_struct_na_base_pair_step.i_auth_asym_id_1 A _ndb_struct_na_base_pair_step.i_auth_seq_id_1 1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 ? _ndb_struct_na_base_pair_step.j_auth_asym_id_1 A _ndb_struct_na_base_pair_step.j_auth_seq_id_1 6 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 ? _ndb_struct_na_base_pair_step.i_auth_asym_id_2 A _ndb_struct_na_base_pair_step.i_auth_seq_id_2 2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 ? _ndb_struct_na_base_pair_step.j_auth_asym_id_2 A _ndb_struct_na_base_pair_step.j_auth_seq_id_2 5 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 ? # _pdbx_initial_refinement_model.accession_code 184D _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.details 'NDB entry udg028' # _atom_sites.entry_id 1QYL _atom_sites.fract_transf_matrix[1][1] 0.044381 _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] 0.017103 _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] 0.041411 _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 V # loop_