data_1DVL # _entry.id 1DVL # _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 1DVL pdb_00001dvl 10.2210/pdb1dvl/pdb NDB DD0024 ? ? RCSB RCSB010410 ? ? WWPDB D_1000010410 ? ? # 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 2002-03-29 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-04 5 'Structure model' 1 4 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' 'Version format compliance' 3 4 'Structure model' 'Refinement description' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 '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' software 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 5 '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 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' 3 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1DVL _pdbx_database_status.recvd_initial_deposition_date 2000-01-21 _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.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Shi, K.' 1 'Mitra, S.N.' 2 'Sundaralingam, M.' 3 # _citation.id primary _citation.title 'Structure of the 1:1 netropsin-decamer d(CCIICICCII)2 complex with a single bound netropsin.' _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume 58 _citation.page_first 601 _citation.page_last 606 _citation.year 2002 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 11914483 _citation.pdbx_database_id_DOI 10.1107/S0907444902001889 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Shi, K.' 1 ? primary 'Mitra, S.N.' 2 ? primary 'Sundaralingam, M.' 3 ? # 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(*CP*CP*IP*IP*CP*IP*CP*CP*IP*I)-3'" 2971.911 2 ? ? ? ? 2 non-polymer syn NETROPSIN 430.464 1 ? ? ? ? 3 water nat water 18.015 31 ? ? ? ? # _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 '(DC)(DC)(DI)(DI)(DC)(DI)(DC)(DC)(DI)(DI)' _entity_poly.pdbx_seq_one_letter_code_can CCIICICCII _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 NETROPSIN NT 3 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 DI n 1 4 DI n 1 5 DC n 1 6 DI n 1 7 DC n 1 8 DC n 1 9 DI n 1 10 DI 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 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DI 'DNA linking' y "2'-DEOXYINOSINE-5'-MONOPHOSPHATE" ? 'C10 H13 N4 O7 P' 332.207 HOH non-polymer . WATER ? 'H2 O' 18.015 NT non-polymer . NETROPSIN ? 'C18 H26 N10 O3' 430.464 # 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 DI 3 3 3 DI I A . n A 1 4 DI 4 4 4 DI I A . n A 1 5 DC 5 5 5 DC C A . n A 1 6 DI 6 6 6 DI I A . n A 1 7 DC 7 7 7 DC C A . n A 1 8 DC 8 8 8 DC C A . n A 1 9 DI 9 9 9 DI I A . n A 1 10 DI 10 10 10 DI I A . n B 1 1 DC 1 11 11 DC C B . n B 1 2 DC 2 12 12 DC C B . n B 1 3 DI 3 13 13 DI I B . n B 1 4 DI 4 14 14 DI I B . n B 1 5 DC 5 15 15 DC C B . n B 1 6 DI 6 16 16 DI I B . n B 1 7 DC 7 17 17 DC C B . n B 1 8 DC 8 18 18 DC C B . n B 1 9 DI 9 19 19 DI I B . n B 1 10 DI 10 20 20 DI I B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 NT 1 25 25 NT NT A . D 3 HOH 1 103 103 HOH HOH A . D 3 HOH 2 106 106 HOH HOH A . D 3 HOH 3 107 107 HOH HOH A . D 3 HOH 4 113 113 HOH HOH A . D 3 HOH 5 115 115 HOH HOH A . D 3 HOH 6 121 121 HOH HOH A . D 3 HOH 7 125 125 HOH HOH A . D 3 HOH 8 128 128 HOH HOH A . D 3 HOH 9 129 129 HOH HOH A . D 3 HOH 10 130 130 HOH HOH A . E 3 HOH 1 101 101 HOH HOH B . E 3 HOH 2 102 102 HOH HOH B . E 3 HOH 3 105 105 HOH HOH B . E 3 HOH 4 108 108 HOH HOH B . E 3 HOH 5 109 109 HOH HOH B . E 3 HOH 6 110 110 HOH HOH B . E 3 HOH 7 111 111 HOH HOH B . E 3 HOH 8 112 112 HOH HOH B . E 3 HOH 9 114 114 HOH HOH B . E 3 HOH 10 116 116 HOH HOH B . E 3 HOH 11 117 117 HOH HOH B . E 3 HOH 12 118 118 HOH HOH B . E 3 HOH 13 119 119 HOH HOH B . E 3 HOH 14 120 120 HOH HOH B . E 3 HOH 15 122 122 HOH HOH B . E 3 HOH 16 123 123 HOH HOH B . E 3 HOH 17 124 124 HOH HOH B . E 3 HOH 18 126 126 HOH HOH B . E 3 HOH 19 127 127 HOH HOH B . E 3 HOH 20 131 131 HOH HOH B . E 3 HOH 21 132 132 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' . ? 1 X-PLOR refinement 3.1 ? 2 X-PLOR phasing . ? 3 # _cell.entry_id 1DVL _cell.length_a 62.400 _cell.length_b 24.470 _cell.length_c 36.310 _cell.angle_alpha 90.00 _cell.angle_beta 110.09 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DVL _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 1DVL _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 40.81 _exptl_crystal.density_Matthews 2.08 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details '4 MM DNA (SINGLE STRAND), 0.008M MGCL2, 0.04 M NA CACODYLATE (PH 6.5), 2MM NETROPSIN, VAPOR DIFFUSION, HANGING DROP at 293K' _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 'SODIUM CACODYLATE' ? ? ? 1 2 1 MGCL2 ? ? ? 1 3 2 MGCL2 ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 293 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IIC' _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 GRAPHITE _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type RIGAKU _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1DVL _reflns.observed_criterion_sigma_I 1.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low ? _reflns.d_resolution_high 2.40 _reflns.number_obs 1795 _reflns.number_all ? _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs 0.0370000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.40 _reflns_shell.d_res_low 2.50 _reflns_shell.percent_possible_all ? _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1DVL _refine.ls_number_reflns_obs 1795 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.0 _refine.ls_d_res_high 2.4 _refine.ls_percent_reflns_obs 85.8 _refine.ls_R_factor_obs 0.1960000 _refine.ls_R_factor_all 0.1960000 _refine.ls_R_factor_R_work 0.1960000 _refine.ls_R_factor_R_free 0.2450000 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10 _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 THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details 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.correlation_coeff_Fo_to_Fc ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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_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 394 _refine_hist.pdbx_number_atoms_ligand 31 _refine_hist.number_atoms_solvent 31 _refine_hist.number_atoms_total 456 _refine_hist.d_res_high 2.4 _refine_hist.d_res_low 8.0 # 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 x_bond_d 0.013 ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg 2.1 ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d 18.6 ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d 1.7 ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 1DVL _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 1DVL _struct.title 'CRYSTAL STRUCTURE OF THE 1:1 NETROPSIN-DECAMER D(CCIICICCII)2 COMPLEX WITH ONLY ONE DRUG BOUND AT ONE END' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1DVL _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DRUG BINDING, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 3 ? E N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1DVL _struct_ref.pdbx_db_accession 1DVL _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 1DVL A 1 ? 10 ? 1DVL 1 ? 10 ? 1 10 2 1 1DVL B 1 ? 10 ? 1DVL 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_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 NT 25 ? 10 'BINDING SITE FOR RESIDUE NT A 25' 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 10 DC A 2 ? DC A 2 . ? 1_555 ? 2 AC1 10 DI A 3 ? DI A 3 . ? 1_555 ? 3 AC1 10 DI A 4 ? DI A 4 . ? 1_555 ? 4 AC1 10 DC A 5 ? DC A 5 . ? 1_555 ? 5 AC1 10 DI A 6 ? DI A 6 . ? 1_555 ? 6 AC1 10 DI B 6 ? DI B 16 . ? 1_555 ? 7 AC1 10 DC B 7 ? DC B 17 . ? 1_555 ? 8 AC1 10 DC B 8 ? DC B 18 . ? 1_555 ? 9 AC1 10 DI B 9 ? DI B 19 . ? 1_555 ? 10 AC1 10 DI B 10 ? DI B 20 . ? 1_555 ? # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 N1 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 DI _pdbx_validate_close_contact.auth_seq_id_1 4 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 N3 _pdbx_validate_close_contact.auth_asym_id_2 B _pdbx_validate_close_contact.auth_comp_id_2 DC _pdbx_validate_close_contact.auth_seq_id_2 17 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.12 # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'MINOR GROOVE BINDER' # 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 DC OP3 O N N 1 DC P P N N 2 DC OP1 O N N 3 DC OP2 O N N 4 DC "O5'" O N N 5 DC "C5'" C N N 6 DC "C4'" C N R 7 DC "O4'" O N N 8 DC "C3'" C N S 9 DC "O3'" O N N 10 DC "C2'" C N N 11 DC "C1'" C N R 12 DC N1 N N N 13 DC C2 C N N 14 DC O2 O N N 15 DC N3 N N N 16 DC C4 C N N 17 DC N4 N N N 18 DC C5 C N N 19 DC C6 C N N 20 DC HOP3 H N N 21 DC HOP2 H N N 22 DC "H5'" H N N 23 DC "H5''" H N N 24 DC "H4'" H N N 25 DC "H3'" H N N 26 DC "HO3'" H N N 27 DC "H2'" H N N 28 DC "H2''" H N N 29 DC "H1'" H N N 30 DC H41 H N N 31 DC H42 H N N 32 DC H5 H N N 33 DC H6 H N N 34 DI OP3 O N N 35 DI P P N N 36 DI OP1 O N N 37 DI OP2 O N N 38 DI "O5'" O N N 39 DI "C5'" C N N 40 DI "C4'" C N R 41 DI "O4'" O N N 42 DI "C3'" C N S 43 DI "O3'" O N N 44 DI "C2'" C N N 45 DI "C1'" C N R 46 DI N9 N Y N 47 DI C8 C Y N 48 DI N7 N Y N 49 DI C5 C Y N 50 DI C6 C N N 51 DI O6 O N N 52 DI N1 N N N 53 DI C2 C N N 54 DI N3 N N N 55 DI C4 C Y N 56 DI HOP3 H N N 57 DI HOP2 H N N 58 DI "H5'" H N N 59 DI "H5''" H N N 60 DI "H4'" H N N 61 DI "H3'" H N N 62 DI "HO3'" H N N 63 DI "H2'" H N N 64 DI "H2''" H N N 65 DI "H1'" H N N 66 DI H8 H N N 67 DI H1 H N N 68 DI H2 H N N 69 HOH O O N N 70 HOH H1 H N N 71 HOH H2 H N N 72 NT C1 C N N 73 NT N1 N N N 74 NT N2 N N N 75 NT N3 N N N 76 NT C2 C N N 77 NT C3 C N N 78 NT O1 O N N 79 NT N4 N N N 80 NT C4 C Y N 81 NT C5 C Y N 82 NT C6 C Y N 83 NT N5 N Y N 84 NT C8 C N N 85 NT C7 C Y N 86 NT C9 C N N 87 NT O2 O N N 88 NT N6 N N N 89 NT C10 C Y N 90 NT C11 C Y N 91 NT C12 C Y N 92 NT N7 N Y N 93 NT C14 C N N 94 NT C13 C Y N 95 NT C15 C N N 96 NT O3 O N N 97 NT N8 N N N 98 NT C16 C N N 99 NT C17 C N N 100 NT C18 C N N 101 NT N9 N N N 102 NT N10 N N N 103 NT HN1 H N N 104 NT HN21 H N N 105 NT HN22 H N N 106 NT HN3 H N N 107 NT H21 H N N 108 NT H22 H N N 109 NT HN4 H N N 110 NT H5 H N N 111 NT H81 H N N 112 NT H82 H N N 113 NT H83 H N N 114 NT H7 H N N 115 NT HN6 H N N 116 NT H11 H N N 117 NT H141 H N N 118 NT H142 H N N 119 NT H143 H N N 120 NT H13 H N N 121 NT HN8 H N N 122 NT H161 H N N 123 NT H162 H N N 124 NT H171 H N N 125 NT H172 H N N 126 NT HN9 H N N 127 NT HN01 H N N 128 NT HN02 H N N 129 # 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 DC OP3 P sing N N 1 DC OP3 HOP3 sing N N 2 DC P OP1 doub N N 3 DC P OP2 sing N N 4 DC P "O5'" sing N N 5 DC OP2 HOP2 sing N N 6 DC "O5'" "C5'" sing N N 7 DC "C5'" "C4'" sing N N 8 DC "C5'" "H5'" sing N N 9 DC "C5'" "H5''" sing N N 10 DC "C4'" "O4'" sing N N 11 DC "C4'" "C3'" sing N N 12 DC "C4'" "H4'" sing N N 13 DC "O4'" "C1'" sing N N 14 DC "C3'" "O3'" sing N N 15 DC "C3'" "C2'" sing N N 16 DC "C3'" "H3'" sing N N 17 DC "O3'" "HO3'" sing N N 18 DC "C2'" "C1'" sing N N 19 DC "C2'" "H2'" sing N N 20 DC "C2'" "H2''" sing N N 21 DC "C1'" N1 sing N N 22 DC "C1'" "H1'" sing N N 23 DC N1 C2 sing N N 24 DC N1 C6 sing N N 25 DC C2 O2 doub N N 26 DC C2 N3 sing N N 27 DC N3 C4 doub N N 28 DC C4 N4 sing N N 29 DC C4 C5 sing N N 30 DC N4 H41 sing N N 31 DC N4 H42 sing N N 32 DC C5 C6 doub N N 33 DC C5 H5 sing N N 34 DC C6 H6 sing N N 35 DI OP3 P sing N N 36 DI OP3 HOP3 sing N N 37 DI P OP1 doub N N 38 DI P OP2 sing N N 39 DI P "O5'" sing N N 40 DI OP2 HOP2 sing N N 41 DI "O5'" "C5'" sing N N 42 DI "C5'" "C4'" sing N N 43 DI "C5'" "H5'" sing N N 44 DI "C5'" "H5''" sing N N 45 DI "C4'" "O4'" sing N N 46 DI "C4'" "C3'" sing N N 47 DI "C4'" "H4'" sing N N 48 DI "O4'" "C1'" sing N N 49 DI "C3'" "O3'" sing N N 50 DI "C3'" "C2'" sing N N 51 DI "C3'" "H3'" sing N N 52 DI "O3'" "HO3'" sing N N 53 DI "C2'" "C1'" sing N N 54 DI "C2'" "H2'" sing N N 55 DI "C2'" "H2''" sing N N 56 DI "C1'" N9 sing N N 57 DI "C1'" "H1'" sing N N 58 DI N9 C8 sing Y N 59 DI N9 C4 sing Y N 60 DI C8 N7 doub Y N 61 DI C8 H8 sing N N 62 DI N7 C5 sing Y N 63 DI C5 C6 sing N N 64 DI C5 C4 doub Y N 65 DI C6 O6 doub N N 66 DI C6 N1 sing N N 67 DI N1 C2 sing N N 68 DI N1 H1 sing N N 69 DI C2 N3 doub N N 70 DI C2 H2 sing N N 71 DI N3 C4 sing N N 72 HOH O H1 sing N N 73 HOH O H2 sing N N 74 NT C1 N1 doub N N 75 NT C1 N2 sing N N 76 NT C1 N3 sing N N 77 NT N1 HN1 sing N N 78 NT N2 HN21 sing N N 79 NT N2 HN22 sing N N 80 NT N3 C2 sing N N 81 NT N3 HN3 sing N N 82 NT C2 C3 sing N N 83 NT C2 H21 sing N N 84 NT C2 H22 sing N N 85 NT C3 O1 doub N N 86 NT C3 N4 sing N N 87 NT N4 C4 sing N N 88 NT N4 HN4 sing N N 89 NT C4 C5 sing Y N 90 NT C4 C7 doub Y N 91 NT C5 C6 doub Y N 92 NT C5 H5 sing N N 93 NT C6 N5 sing Y N 94 NT C6 C9 sing N N 95 NT N5 C8 sing N N 96 NT N5 C7 sing Y N 97 NT C8 H81 sing N N 98 NT C8 H82 sing N N 99 NT C8 H83 sing N N 100 NT C7 H7 sing N N 101 NT C9 O2 doub N N 102 NT C9 N6 sing N N 103 NT N6 C10 sing N N 104 NT N6 HN6 sing N N 105 NT C10 C11 sing Y N 106 NT C10 C13 doub Y N 107 NT C11 C12 doub Y N 108 NT C11 H11 sing N N 109 NT C12 N7 sing Y N 110 NT C12 C15 sing N N 111 NT N7 C14 sing N N 112 NT N7 C13 sing Y N 113 NT C14 H141 sing N N 114 NT C14 H142 sing N N 115 NT C14 H143 sing N N 116 NT C13 H13 sing N N 117 NT C15 O3 doub N N 118 NT C15 N8 sing N N 119 NT N8 C16 sing N N 120 NT N8 HN8 sing N N 121 NT C16 C17 sing N N 122 NT C16 H161 sing N N 123 NT C16 H162 sing N N 124 NT C17 C18 sing N N 125 NT C17 H171 sing N N 126 NT C17 H172 sing N N 127 NT C18 N9 doub N N 128 NT C18 N10 sing N N 129 NT N9 HN9 sing N N 130 NT N10 HN01 sing N N 131 NT N10 HN02 sing N N 132 # _atom_sites.entry_id 1DVL _atom_sites.fract_transf_matrix[1][1] 0.016026 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.005861 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.040866 _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] 0.029325 _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_