data_1A2E # _entry.id 1A2E # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.385 _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 1A2E pdb_00001a2e 10.2210/pdb1a2e/pdb RCSB DDJ075 ? ? WWPDB D_1000170308 ? ? # 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 1999-04-12 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-07 # _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' 'Non-polymer description' 3 3 'Structure model' 'Version format compliance' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Database references' 6 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 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' struct_conn 5 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 4 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 5 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 6 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 7 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 8 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 9 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 10 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 11 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 12 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 13 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 14 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 15 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 16 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 17 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 18 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 19 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1A2E _pdbx_database_status.recvd_initial_deposition_date 1998-01-05 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _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.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Coste, F.' 1 'Zelwer, C.' 2 # _citation.id primary _citation.title ;Crystal structure of a double-stranded DNA containing a cisplatin interstrand cross-link at 1.63 A resolution: hydration at the platinated site. ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 27 _citation.page_first 1837 _citation.page_last 1846 _citation.year 1999 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 10101191 _citation.pdbx_database_id_DOI 10.1093/nar/27.8.1837 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Coste, F.' 1 ? primary 'Malinge, J.M.' 2 ? primary 'Serre, L.' 3 ? primary 'Shepard, W.' 4 ? primary 'Roth, M.' 5 ? primary 'Leng, M.' 6 ? primary 'Zelwer, C.' 7 ? # 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(*CP*CP*TP*CP*GP*CP*TP*CP*TP*C)-3') ; 2931.917 1 ? ? ? 'PT(CPT) CROSSLINKS N7(G5) AND N7(G15)' 2 polymer syn ;DNA (5'-D(*GP*AP*GP*AP*GP*CP*GP*AP*GP*G)-3') ; 3159.079 1 ? ? ? 'PT(CPT) CROSSLINKS N7(G5) AND N7(G15)' 3 non-polymer syn Cisplatin 300.045 1 ? ? ? ? 4 water nat water 18.015 92 ? ? ? ? # 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 '(DC)(DC)(DT)(DC)(DG)(DC)(DT)(DC)(DT)(DC)' CCTCGCTCTC A ? 2 polydeoxyribonucleotide no no '(DG)(DA)(DG)(DA)(DG)(DC)(DG)(DA)(DG)(DG)' GAGAGCGAGG B ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 Cisplatin CPT 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DC n 1 3 DT n 1 4 DC n 1 5 DG n 1 6 DC n 1 7 DT n 1 8 DC n 1 9 DT n 1 10 DC n 2 1 DG n 2 2 DA n 2 3 DG n 2 4 DA n 2 5 DG n 2 6 DC n 2 7 DG n 2 8 DA n 2 9 DG n 2 10 DG 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 CPT non-polymer . Cisplatin 'diammine(dichloro)platinum' 'Cl2 H6 N2 Pt' 300.045 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 # 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 DC 1 1 1 DC C A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DT 3 3 3 DT T A . n A 1 4 DC 4 4 4 DC C 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 A 1 8 DC 8 8 8 DC C A . n A 1 9 DT 9 9 9 DT T A . n A 1 10 DC 10 10 10 DC C A . n B 2 1 DG 1 11 11 DG G B . n B 2 2 DA 2 12 12 DA A B . n B 2 3 DG 3 13 13 DG G B . n B 2 4 DA 4 14 14 DA A B . n B 2 5 DG 5 15 15 DG G B . n B 2 6 DC 6 16 16 DC C B . n B 2 7 DG 7 17 17 DG G B . n B 2 8 DA 8 18 18 DA A B . n B 2 9 DG 9 19 19 DG G B . n B 2 10 DG 10 20 20 DG G 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 3 CPT 1 101 101 CPT CPT A . D 4 HOH 1 102 1 HOH HOH A . D 4 HOH 2 103 2 HOH HOH A . D 4 HOH 3 104 5 HOH HOH A . D 4 HOH 4 105 7 HOH HOH A . D 4 HOH 5 106 9 HOH HOH A . D 4 HOH 6 107 10 HOH HOH A . D 4 HOH 7 108 11 HOH HOH A . D 4 HOH 8 109 15 HOH HOH A . D 4 HOH 9 110 16 HOH HOH A . D 4 HOH 10 111 17 HOH HOH A . D 4 HOH 11 112 20 HOH HOH A . D 4 HOH 12 113 21 HOH HOH A . D 4 HOH 13 114 22 HOH HOH A . D 4 HOH 14 115 23 HOH HOH A . D 4 HOH 15 116 24 HOH HOH A . D 4 HOH 16 117 29 HOH HOH A . D 4 HOH 17 118 30 HOH HOH A . D 4 HOH 18 119 31 HOH HOH A . D 4 HOH 19 120 33 HOH HOH A . D 4 HOH 20 121 36 HOH HOH A . D 4 HOH 21 122 37 HOH HOH A . D 4 HOH 22 123 41 HOH HOH A . D 4 HOH 23 124 42 HOH HOH A . D 4 HOH 24 125 43 HOH HOH A . D 4 HOH 25 126 45 HOH HOH A . D 4 HOH 26 127 48 HOH HOH A . D 4 HOH 27 128 49 HOH HOH A . D 4 HOH 28 129 53 HOH HOH A . D 4 HOH 29 130 56 HOH HOH A . D 4 HOH 30 131 58 HOH HOH A . D 4 HOH 31 132 59 HOH HOH A . D 4 HOH 32 133 61 HOH HOH A . D 4 HOH 33 134 63 HOH HOH A . D 4 HOH 34 135 69 HOH HOH A . D 4 HOH 35 136 71 HOH HOH A . D 4 HOH 36 137 72 HOH HOH A . D 4 HOH 37 138 73 HOH HOH A . D 4 HOH 38 139 75 HOH HOH A . D 4 HOH 39 140 76 HOH HOH A . D 4 HOH 40 141 78 HOH HOH A . D 4 HOH 41 142 79 HOH HOH A . D 4 HOH 42 143 80 HOH HOH A . D 4 HOH 43 144 81 HOH HOH A . D 4 HOH 44 145 82 HOH HOH A . D 4 HOH 45 146 84 HOH HOH A . D 4 HOH 46 147 85 HOH HOH A . D 4 HOH 47 148 86 HOH HOH A . D 4 HOH 48 149 88 HOH HOH A . D 4 HOH 49 150 89 HOH HOH A . D 4 HOH 50 151 90 HOH HOH A . E 4 HOH 1 21 3 HOH HOH B . E 4 HOH 2 22 4 HOH HOH B . E 4 HOH 3 23 6 HOH HOH B . E 4 HOH 4 24 8 HOH HOH B . E 4 HOH 5 25 12 HOH HOH B . E 4 HOH 6 26 13 HOH HOH B . E 4 HOH 7 27 14 HOH HOH B . E 4 HOH 8 28 18 HOH HOH B . E 4 HOH 9 29 19 HOH HOH B . E 4 HOH 10 30 25 HOH HOH B . E 4 HOH 11 31 26 HOH HOH B . E 4 HOH 12 32 27 HOH HOH B . E 4 HOH 13 33 28 HOH HOH B . E 4 HOH 14 34 32 HOH HOH B . E 4 HOH 15 35 34 HOH HOH B . E 4 HOH 16 36 35 HOH HOH B . E 4 HOH 17 37 38 HOH HOH B . E 4 HOH 18 38 39 HOH HOH B . E 4 HOH 19 39 40 HOH HOH B . E 4 HOH 20 40 44 HOH HOH B . E 4 HOH 21 41 46 HOH HOH B . E 4 HOH 22 42 47 HOH HOH B . E 4 HOH 23 43 50 HOH HOH B . E 4 HOH 24 44 51 HOH HOH B . E 4 HOH 25 45 52 HOH HOH B . E 4 HOH 26 46 54 HOH HOH B . E 4 HOH 27 47 55 HOH HOH B . E 4 HOH 28 48 57 HOH HOH B . E 4 HOH 29 49 60 HOH HOH B . E 4 HOH 30 50 62 HOH HOH B . E 4 HOH 31 51 64 HOH HOH B . E 4 HOH 32 52 65 HOH HOH B . E 4 HOH 33 53 66 HOH HOH B . E 4 HOH 34 54 67 HOH HOH B . E 4 HOH 35 55 68 HOH HOH B . E 4 HOH 36 56 70 HOH HOH B . E 4 HOH 37 57 74 HOH HOH B . E 4 HOH 38 58 77 HOH HOH B . E 4 HOH 39 59 83 HOH HOH B . E 4 HOH 40 60 87 HOH HOH B . E 4 HOH 41 61 91 HOH HOH B . E 4 HOH 42 62 92 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHARP phasing . ? 1 SHELXL-96 refinement . ? 2 MOSFLM 'data reduction' . ? 3 CCP4 'data scaling' '(SCALA)' ? 4 # _cell.entry_id 1A2E _cell.length_a 42.890 _cell.length_b 29.980 _cell.length_c 46.570 _cell.angle_alpha 90.00 _cell.angle_beta 95.98 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1A2E _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting monoclinic _symmetry.Int_Tables_number 5 # _exptl.entry_id 1A2E _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.34 _exptl_crystal.density_percent_sol 56.0000 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.20 _exptl_crystal_grow.pdbx_details 'pH 6.20' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100.00 _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 1997-11-01 _diffrn_detector.details MIRRORS # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'DOUBLE CRYSTAL' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0711 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'LURE BEAMLINE DW21B' _diffrn_source.pdbx_synchrotron_site LURE _diffrn_source.pdbx_synchrotron_beamline DW21B _diffrn_source.pdbx_wavelength 1.0711 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1A2E _reflns.observed_criterion_sigma_I 4.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 46.130 _reflns.d_resolution_high 1.630 _reflns.number_obs 7353 _reflns.number_all ? _reflns.percent_possible_obs 93.100 _reflns.pdbx_Rmerge_I_obs 0.0370000 _reflns.pdbx_Rsym_value 0.0370000 _reflns.pdbx_netI_over_sigmaI 6.000 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 3.500 _reflns.R_free_details ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.630 _reflns_shell.d_res_low 1.720 _reflns_shell.percent_possible_all 91.00 _reflns_shell.Rmerge_I_obs 0.0630000 _reflns_shell.pdbx_Rsym_value 0.0490000 _reflns_shell.meanI_over_sigI_obs 12.00 _reflns_shell.pdbx_redundancy 3.100 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 1A2E _refine.ls_number_reflns_obs 6983 _refine.ls_number_reflns_all 6983 _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 20.0 _refine.ls_d_res_high 1.63 _refine.ls_percent_reflns_obs 93.1 _refine.ls_R_factor_obs 0.1692000 _refine.ls_R_factor_all 0.1692000 _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 2176 _refine.ls_number_restraints 2201 _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 'MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-223' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method 'FREE R' _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values NUCLSQ _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.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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _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 1A2E _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 ? _refine_analyze.occupancy_sum_hydrogen 479.67 _refine_analyze.occupancy_sum_non_hydrogen ? _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 404 _refine_hist.pdbx_number_atoms_ligand 3 _refine_hist.number_atoms_solvent 92 _refine_hist.number_atoms_total 499 _refine_hist.d_res_high 1.63 _refine_hist.d_res_low 20.0 # 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 0.010 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.031 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist ? ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes 0.026 ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol 0.062 ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr 0.009 ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt 0.098 ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps ? ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 1A2E _pdbx_refine.R_factor_all_no_cutoff ? _pdbx_refine.R_factor_obs_no_cutoff 0.1692000 _pdbx_refine.free_R_factor_no_cutoff 0.2032000 _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 5.00 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 340 _pdbx_refine.R_factor_all_4sig_cutoff ? _pdbx_refine.R_factor_obs_4sig_cutoff 0.1673000 _pdbx_refine.free_R_factor_4sig_cutoff 0.2023000 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 5.00 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 334 _pdbx_refine.number_reflns_obs_4sig_cutoff 6758 _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 1A2E _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 1A2E _struct.title 'CRYSTAL STRUCTURE OF A DOUBLE-STRANDED DNA DECAMER CONTAINING A CISPLATIN INTERSTRAND CROSS-LINK ADDUCT' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1A2E _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'ANTITUMOR DRUG, CIS-DDP, INTERSTRAND CROSS-LINK, 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 ? D N N 4 ? E N N 4 ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 1A2E 1A2E ? ? ? 2 2 PDB 1A2E 1A2E ? ? ? # 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 1A2E A 1 ? 10 ? 1A2E 1 ? 10 ? 1 10 2 2 1A2E B 1 ? 10 ? 1A2E 11 ? 20 ? 11 20 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # _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.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 ? ? A DG 5 N7 ? ? ? 1_555 C CPT . PT1 ? ? A DG 5 A CPT 101 1_555 ? ? ? ? ? ? ? 2.000 ? ? metalc2 metalc ? ? C CPT . PT1 ? ? ? 1_555 B DG 5 N7 ? ? A CPT 101 B DG 15 1_555 ? ? ? ? ? ? ? 1.999 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 8 N1 ? ? A DT 3 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 8 N6 ? ? A DT 3 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 4 N3 ? ? ? 1_555 B DG 7 N1 ? ? A DC 4 B DG 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B DG 7 O6 ? ? A DC 4 B DG 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DG 7 N2 ? ? A DC 4 B DG 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 7 B DA 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 7 B DA 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B DA 2 N1 ? ? A DT 9 B DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B DA 2 N6 ? ? A DT 9 B DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # 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 N7 ? A DG 5 ? A DG 5 ? 1_555 PT1 ? C CPT . ? A CPT 101 ? 1_555 N1 ? C CPT . ? A CPT 101 ? 1_555 90.8 ? 2 N7 ? A DG 5 ? A DG 5 ? 1_555 PT1 ? C CPT . ? A CPT 101 ? 1_555 N2 ? C CPT . ? A CPT 101 ? 1_555 179.7 ? 3 N1 ? C CPT . ? A CPT 101 ? 1_555 PT1 ? C CPT . ? A CPT 101 ? 1_555 N2 ? C CPT . ? A CPT 101 ? 1_555 89.0 ? 4 N7 ? A DG 5 ? A DG 5 ? 1_555 PT1 ? C CPT . ? A CPT 101 ? 1_555 N7 ? B DG 5 ? B DG 15 ? 1_555 86.8 ? 5 N1 ? C CPT . ? A CPT 101 ? 1_555 PT1 ? C CPT . ? A CPT 101 ? 1_555 N7 ? B DG 5 ? B DG 15 ? 1_555 177.6 ? 6 N2 ? C CPT . ? A CPT 101 ? 1_555 PT1 ? C CPT . ? A CPT 101 ? 1_555 N7 ? B DG 5 ? B DG 15 ? 1_555 93.4 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A CPT 101 ? 8 'BINDING SITE FOR RESIDUE CPT A 101' 1 ? ? ? ? ? ? ? # 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 8 DG A 5 ? DG A 5 . ? 1_555 ? 2 AC1 8 DT A 7 ? DT A 7 . ? 1_555 ? 3 AC1 8 DC A 8 ? DC A 8 . ? 1_555 ? 4 AC1 8 HOH D . ? HOH A 106 . ? 1_555 ? 5 AC1 8 HOH D . ? HOH A 135 . ? 1_555 ? 6 AC1 8 DG B 5 ? DG B 15 . ? 1_555 ? 7 AC1 8 DG B 7 ? DG B 17 . ? 1_555 ? 8 AC1 8 HOH E . ? HOH B 25 . ? 1_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'" B DA 14 ? ? "C1'" B DA 14 ? ? 1.489 1.420 0.069 0.011 N 2 1 "O4'" B DG 17 ? ? "C1'" B DG 17 ? ? 1.497 1.420 0.077 0.011 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 DC 1 ? ? "C4'" A DC 1 ? ? "C3'" A DC 1 ? ? 101.43 104.50 -3.07 0.40 N 2 1 "O4'" A DC 2 ? ? "C4'" A DC 2 ? ? "C3'" A DC 2 ? ? 101.48 104.50 -3.02 0.40 N 3 1 C5 A DC 2 ? ? C6 A DC 2 ? ? N1 A DC 2 ? ? 117.11 121.00 -3.89 0.50 N 4 1 "O4'" A DT 3 ? ? "C4'" A DT 3 ? ? "C3'" A DT 3 ? ? 101.98 104.50 -2.52 0.40 N 5 1 "O5'" A DC 4 ? ? "C5'" A DC 4 ? ? "C4'" A DC 4 ? ? 102.87 109.40 -6.53 0.80 N 6 1 "O4'" A DC 4 ? ? "C1'" A DC 4 ? ? N1 A DC 4 ? ? 110.17 108.30 1.87 0.30 N 7 1 "C3'" A DG 5 ? ? "O3'" A DG 5 ? ? P A DC 6 ? ? 127.43 119.70 7.73 1.20 Y 8 1 "O4'" A DC 6 ? ? "C1'" A DC 6 ? ? N1 A DC 6 ? ? 101.33 108.00 -6.67 0.70 N 9 1 "C3'" A DC 6 ? ? "O3'" A DC 6 ? ? P A DT 7 ? ? 129.81 119.70 10.11 1.20 Y 10 1 "O5'" A DT 7 ? ? "C5'" A DT 7 ? ? "C4'" A DT 7 ? ? 104.21 109.40 -5.19 0.80 N 11 1 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 101.94 108.00 -6.06 0.70 N 12 1 "O4'" A DT 9 ? ? "C4'" A DT 9 ? ? "C3'" A DT 9 ? ? 101.43 104.50 -3.07 0.40 N 13 1 "O4'" A DC 10 ? ? "C4'" A DC 10 ? ? "C3'" A DC 10 ? ? 99.79 104.50 -4.71 0.40 N 14 1 "O5'" B DG 11 ? ? "C5'" B DG 11 ? ? "C4'" B DG 11 ? ? 103.46 109.40 -5.94 0.80 N 15 1 "O4'" B DG 11 ? ? "C4'" B DG 11 ? ? "C3'" B DG 11 ? ? 101.69 104.50 -2.81 0.40 N 16 1 N1 B DG 11 ? ? C6 B DG 11 ? ? O6 B DG 11 ? ? 115.88 119.90 -4.02 0.60 N 17 1 "O5'" B DA 12 ? ? "C5'" B DA 12 ? ? "C4'" B DA 12 ? ? 100.84 109.40 -8.56 0.80 N 18 1 "O4'" B DA 12 ? ? "C1'" B DA 12 ? ? N9 B DA 12 ? ? 112.75 108.30 4.45 0.30 N 19 1 "C3'" B DA 12 ? ? "O3'" B DA 12 ? ? P B DG 13 ? ? 135.48 119.70 15.78 1.20 Y 20 1 N1 B DG 13 ? ? C6 B DG 13 ? ? O6 B DG 13 ? ? 124.23 119.90 4.33 0.60 N 21 1 "O5'" B DA 14 ? ? "C5'" B DA 14 ? ? "C4'" B DA 14 ? ? 104.05 109.40 -5.35 0.80 N 22 1 "O4'" B DG 15 ? ? "C4'" B DG 15 ? ? "C3'" B DG 15 ? ? 101.67 104.50 -2.83 0.40 N 23 1 "O4'" B DG 15 ? ? "C1'" B DG 15 ? ? N9 B DG 15 ? ? 111.45 108.30 3.15 0.30 N 24 1 "O5'" B DC 16 ? ? "C5'" B DC 16 ? ? "C4'" B DC 16 ? ? 103.28 109.40 -6.12 0.80 N 25 1 "O4'" B DG 17 ? ? "C4'" B DG 17 ? ? "C3'" B DG 17 ? ? 101.66 104.50 -2.84 0.40 N 26 1 "O4'" B DG 17 ? ? "C1'" B DG 17 ? ? N9 B DG 17 ? ? 101.91 108.00 -6.09 0.70 N 27 1 "C3'" B DG 17 ? ? "O3'" B DG 17 ? ? P B DA 18 ? ? 126.94 119.70 7.24 1.20 Y 28 1 "O5'" B DA 18 ? ? "C5'" B DA 18 ? ? "C4'" B DA 18 ? ? 104.53 109.40 -4.87 0.80 N 29 1 "O4'" B DA 18 ? ? "C1'" B DA 18 ? ? "C2'" B DA 18 ? ? 101.08 105.90 -4.82 0.80 N 30 1 "O4'" B DA 18 ? ? "C1'" B DA 18 ? ? N9 B DA 18 ? ? 114.04 108.30 5.74 0.30 N 31 1 "O4'" B DG 19 ? ? "C4'" B DG 19 ? ? "C3'" B DG 19 ? ? 101.92 104.50 -2.58 0.40 N 32 1 "O5'" B DG 20 ? ? "C5'" B DG 20 ? ? "C4'" B DG 20 ? ? 104.18 109.40 -5.22 0.80 N # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'COVALENT PT-N BONDS' # 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 CPT PT1 PT N N 1 CPT N1 N N N 2 CPT N2 N N N 3 CPT H11 H N N 4 CPT H12 H N N 5 CPT H21 H N N 6 CPT H22 H N N 7 CPT CL2 CL N N 8 CPT CL1 CL N N 9 CPT H13 H N N 10 CPT H23 H N N 11 DA OP3 O N N 12 DA P P N N 13 DA OP1 O N N 14 DA OP2 O N N 15 DA "O5'" O N N 16 DA "C5'" C N N 17 DA "C4'" C N R 18 DA "O4'" O N N 19 DA "C3'" C N S 20 DA "O3'" O N N 21 DA "C2'" C N N 22 DA "C1'" C N R 23 DA N9 N Y N 24 DA C8 C Y N 25 DA N7 N Y N 26 DA C5 C Y N 27 DA C6 C Y N 28 DA N6 N N N 29 DA N1 N Y N 30 DA C2 C Y N 31 DA N3 N Y N 32 DA C4 C Y N 33 DA HOP3 H N N 34 DA HOP2 H N N 35 DA "H5'" H N N 36 DA "H5''" H N N 37 DA "H4'" H N N 38 DA "H3'" H N N 39 DA "HO3'" H N N 40 DA "H2'" H N N 41 DA "H2''" H N N 42 DA "H1'" H N N 43 DA H8 H N N 44 DA H61 H N N 45 DA H62 H N N 46 DA H2 H N N 47 DC OP3 O N N 48 DC P P N N 49 DC OP1 O N N 50 DC OP2 O N N 51 DC "O5'" O N N 52 DC "C5'" C N N 53 DC "C4'" C N R 54 DC "O4'" O N N 55 DC "C3'" C N S 56 DC "O3'" O N N 57 DC "C2'" C N N 58 DC "C1'" C N R 59 DC N1 N N N 60 DC C2 C N N 61 DC O2 O N N 62 DC N3 N N N 63 DC C4 C N N 64 DC N4 N N N 65 DC C5 C N N 66 DC C6 C N N 67 DC HOP3 H N N 68 DC HOP2 H N N 69 DC "H5'" H N N 70 DC "H5''" H N N 71 DC "H4'" H N N 72 DC "H3'" H N N 73 DC "HO3'" H N N 74 DC "H2'" H N N 75 DC "H2''" H N N 76 DC "H1'" H N N 77 DC H41 H N N 78 DC H42 H N N 79 DC H5 H N N 80 DC H6 H N N 81 DG OP3 O N N 82 DG P P N N 83 DG OP1 O N N 84 DG OP2 O N N 85 DG "O5'" O N N 86 DG "C5'" C N N 87 DG "C4'" C N R 88 DG "O4'" O N N 89 DG "C3'" C N S 90 DG "O3'" O N N 91 DG "C2'" C N N 92 DG "C1'" C N R 93 DG N9 N Y N 94 DG C8 C Y N 95 DG N7 N Y N 96 DG C5 C Y N 97 DG C6 C N N 98 DG O6 O N N 99 DG N1 N N N 100 DG C2 C N N 101 DG N2 N N N 102 DG N3 N N N 103 DG C4 C Y N 104 DG HOP3 H N N 105 DG HOP2 H N N 106 DG "H5'" H N N 107 DG "H5''" H N N 108 DG "H4'" H N N 109 DG "H3'" H N N 110 DG "HO3'" H N N 111 DG "H2'" H N N 112 DG "H2''" H N N 113 DG "H1'" H N N 114 DG H8 H N N 115 DG H1 H N N 116 DG H21 H N N 117 DG H22 H N N 118 DT OP3 O N N 119 DT P P N N 120 DT OP1 O N N 121 DT OP2 O N N 122 DT "O5'" O N N 123 DT "C5'" C N N 124 DT "C4'" C N R 125 DT "O4'" O N N 126 DT "C3'" C N S 127 DT "O3'" O N N 128 DT "C2'" C N N 129 DT "C1'" C N R 130 DT N1 N N N 131 DT C2 C N N 132 DT O2 O N N 133 DT N3 N N N 134 DT C4 C N N 135 DT O4 O N N 136 DT C5 C N N 137 DT C7 C N N 138 DT C6 C N N 139 DT HOP3 H N N 140 DT HOP2 H N N 141 DT "H5'" H N N 142 DT "H5''" H N N 143 DT "H4'" H N N 144 DT "H3'" H N N 145 DT "HO3'" H N N 146 DT "H2'" H N N 147 DT "H2''" H N N 148 DT "H1'" H N N 149 DT H3 H N N 150 DT H71 H N N 151 DT H72 H N N 152 DT H73 H N N 153 DT H6 H N N 154 HOH O O N N 155 HOH H1 H N N 156 HOH H2 H N N 157 # 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 CPT PT1 N1 sing N N 1 CPT PT1 N2 sing N N 2 CPT N1 H11 sing N N 3 CPT N1 H12 sing N N 4 CPT N1 H13 sing N N 5 CPT N2 H21 sing N N 6 CPT N2 H22 sing N N 7 CPT N2 H23 sing N N 8 CPT CL2 PT1 sing N N 9 CPT CL1 PT1 sing N N 10 DA OP3 P sing N N 11 DA OP3 HOP3 sing N N 12 DA P OP1 doub N N 13 DA P OP2 sing N N 14 DA P "O5'" sing N N 15 DA OP2 HOP2 sing N N 16 DA "O5'" "C5'" sing N N 17 DA "C5'" "C4'" sing N N 18 DA "C5'" "H5'" sing N N 19 DA "C5'" "H5''" sing N N 20 DA "C4'" "O4'" sing N N 21 DA "C4'" "C3'" sing N N 22 DA "C4'" "H4'" sing N N 23 DA "O4'" "C1'" sing N N 24 DA "C3'" "O3'" sing N N 25 DA "C3'" "C2'" sing N N 26 DA "C3'" "H3'" sing N N 27 DA "O3'" "HO3'" sing N N 28 DA "C2'" "C1'" sing N N 29 DA "C2'" "H2'" sing N N 30 DA "C2'" "H2''" sing N N 31 DA "C1'" N9 sing N N 32 DA "C1'" "H1'" sing N N 33 DA N9 C8 sing Y N 34 DA N9 C4 sing Y N 35 DA C8 N7 doub Y N 36 DA C8 H8 sing N N 37 DA N7 C5 sing Y N 38 DA C5 C6 sing Y N 39 DA C5 C4 doub Y N 40 DA C6 N6 sing N N 41 DA C6 N1 doub Y N 42 DA N6 H61 sing N N 43 DA N6 H62 sing N N 44 DA N1 C2 sing Y N 45 DA C2 N3 doub Y N 46 DA C2 H2 sing N N 47 DA N3 C4 sing Y N 48 DC OP3 P sing N N 49 DC OP3 HOP3 sing N N 50 DC P OP1 doub N N 51 DC P OP2 sing N N 52 DC P "O5'" sing N N 53 DC OP2 HOP2 sing N N 54 DC "O5'" "C5'" sing N N 55 DC "C5'" "C4'" sing N N 56 DC "C5'" "H5'" sing N N 57 DC "C5'" "H5''" sing N N 58 DC "C4'" "O4'" sing N N 59 DC "C4'" "C3'" sing N N 60 DC "C4'" "H4'" sing N N 61 DC "O4'" "C1'" sing N N 62 DC "C3'" "O3'" sing N N 63 DC "C3'" "C2'" sing N N 64 DC "C3'" "H3'" sing N N 65 DC "O3'" "HO3'" sing N N 66 DC "C2'" "C1'" sing N N 67 DC "C2'" "H2'" sing N N 68 DC "C2'" "H2''" sing N N 69 DC "C1'" N1 sing N N 70 DC "C1'" "H1'" sing N N 71 DC N1 C2 sing N N 72 DC N1 C6 sing N N 73 DC C2 O2 doub N N 74 DC C2 N3 sing N N 75 DC N3 C4 doub N N 76 DC C4 N4 sing N N 77 DC C4 C5 sing N N 78 DC N4 H41 sing N N 79 DC N4 H42 sing N N 80 DC C5 C6 doub N N 81 DC C5 H5 sing N N 82 DC C6 H6 sing N N 83 DG OP3 P sing N N 84 DG OP3 HOP3 sing N N 85 DG P OP1 doub N N 86 DG P OP2 sing N N 87 DG P "O5'" sing N N 88 DG OP2 HOP2 sing N N 89 DG "O5'" "C5'" sing N N 90 DG "C5'" "C4'" sing N N 91 DG "C5'" "H5'" sing N N 92 DG "C5'" "H5''" sing N N 93 DG "C4'" "O4'" sing N N 94 DG "C4'" "C3'" sing N N 95 DG "C4'" "H4'" sing N N 96 DG "O4'" "C1'" sing N N 97 DG "C3'" "O3'" sing N N 98 DG "C3'" "C2'" sing N N 99 DG "C3'" "H3'" sing N N 100 DG "O3'" "HO3'" sing N N 101 DG "C2'" "C1'" sing N N 102 DG "C2'" "H2'" sing N N 103 DG "C2'" "H2''" sing N N 104 DG "C1'" N9 sing N N 105 DG "C1'" "H1'" sing N N 106 DG N9 C8 sing Y N 107 DG N9 C4 sing Y N 108 DG C8 N7 doub Y N 109 DG C8 H8 sing N N 110 DG N7 C5 sing Y N 111 DG C5 C6 sing N N 112 DG C5 C4 doub Y N 113 DG C6 O6 doub N N 114 DG C6 N1 sing N N 115 DG N1 C2 sing N N 116 DG N1 H1 sing N N 117 DG C2 N2 sing N N 118 DG C2 N3 doub N N 119 DG N2 H21 sing N N 120 DG N2 H22 sing N N 121 DG N3 C4 sing N N 122 DT OP3 P sing N N 123 DT OP3 HOP3 sing N N 124 DT P OP1 doub N N 125 DT P OP2 sing N N 126 DT P "O5'" sing N N 127 DT OP2 HOP2 sing N N 128 DT "O5'" "C5'" sing N N 129 DT "C5'" "C4'" sing N N 130 DT "C5'" "H5'" sing N N 131 DT "C5'" "H5''" sing N N 132 DT "C4'" "O4'" sing N N 133 DT "C4'" "C3'" sing N N 134 DT "C4'" "H4'" sing N N 135 DT "O4'" "C1'" sing N N 136 DT "C3'" "O3'" sing N N 137 DT "C3'" "C2'" sing N N 138 DT "C3'" "H3'" sing N N 139 DT "O3'" "HO3'" sing N N 140 DT "C2'" "C1'" sing N N 141 DT "C2'" "H2'" sing N N 142 DT "C2'" "H2''" sing N N 143 DT "C1'" N1 sing N N 144 DT "C1'" "H1'" sing N N 145 DT N1 C2 sing N N 146 DT N1 C6 sing N N 147 DT C2 O2 doub N N 148 DT C2 N3 sing N N 149 DT N3 C4 sing N N 150 DT N3 H3 sing N N 151 DT C4 O4 doub N N 152 DT C4 C5 sing N N 153 DT C5 C7 sing N N 154 DT C5 C6 doub N N 155 DT C7 H71 sing N N 156 DT C7 H72 sing N N 157 DT C7 H73 sing N N 158 DT C6 H6 sing N N 159 HOH O H1 sing N N 160 HOH O H2 sing N N 161 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1A2E 'double helix' 1A2E 'b-form double helix' 1A2E 'internal 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 DC 1 1_555 B DG 10 1_555 0.293 -0.153 0.205 -8.313 -10.795 -0.174 1 A_DC1:DG20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.161 -0.015 0.339 -5.484 -7.806 -0.270 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DT 3 1_555 B DA 8 1_555 -0.248 -0.049 -0.117 -2.121 -5.868 4.536 3 A_DT3:DA18_B A 3 ? B 18 ? 20 1 1 A DC 4 1_555 B DG 7 1_555 0.258 -0.067 -0.421 15.321 0.077 -4.090 4 A_DC4:DG17_B A 4 ? B 17 ? 19 1 1 A DT 7 1_555 B DA 4 1_555 -0.063 -0.009 0.084 -9.662 -8.608 2.523 5 A_DT7:DA14_B A 7 ? B 14 ? 20 1 1 A DC 8 1_555 B DG 3 1_555 0.315 -0.187 0.045 -8.926 -9.275 -0.264 6 A_DC8:DG13_B A 8 ? B 13 ? 19 1 1 A DT 9 1_555 B DA 2 1_555 -0.152 -0.092 -0.004 -10.837 -7.204 -2.005 7 A_DT9:DA12_B A 9 ? B 12 ? 20 1 1 A DC 10 1_555 B DG 1 1_555 0.187 -0.159 -0.238 -0.156 -5.033 -2.469 8 A_DC10:DG11_B A 10 ? B 11 ? 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 DC 1 1_555 B DG 10 1_555 A DC 2 1_555 B DG 9 1_555 0.642 -1.340 3.309 0.711 1.557 36.328 -2.365 -0.930 3.262 2.496 -1.139 36.367 1 AA_DC1DC2:DG19DG20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DC 2 1_555 B DG 9 1_555 A DT 3 1_555 B DA 8 1_555 -1.371 -1.032 3.360 4.516 1.573 20.506 -3.468 5.598 2.907 4.342 -12.469 21.050 2 AA_DC2DT3:DA18DG19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DT 3 1_555 B DA 8 1_555 A DC 4 1_555 B DG 7 1_555 -0.759 0.733 3.089 6.166 15.194 23.197 -1.972 2.958 2.762 33.011 -13.398 28.342 3 AA_DT3DC4:DG17DA18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DT 7 1_555 B DA 4 1_555 A DC 8 1_555 B DG 3 1_555 -0.388 -0.061 3.220 -0.455 0.802 38.001 -0.195 0.539 3.223 1.231 0.699 38.012 4 AA_DT7DC8:DG13DA14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A DC 8 1_555 B DG 3 1_555 A DT 9 1_555 B DA 2 1_555 0.988 0.040 3.250 4.930 2.887 34.678 -0.372 -0.889 3.347 4.803 -8.202 35.131 5 AA_DC8DT9:DA12DG13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DT 9 1_555 B DA 2 1_555 A DC 10 1_555 B DG 1 1_555 -0.020 -0.041 3.062 2.652 0.780 29.843 -0.230 0.551 3.047 1.510 -5.136 29.968 6 AA_DT9DC10:DG11DA12_BB A 9 ? B 12 ? A 10 ? B 11 ? # _atom_sites.entry_id 1A2E _atom_sites.fract_transf_matrix[1][1] 0.023315 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.002442 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.033356 _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] 0.021591 _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 PT # loop_