data_1K2Z # _entry.id 1K2Z # _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 1K2Z pdb_00001k2z 10.2210/pdb1k2z/pdb NDB DD0046 ? ? RCSB RCSB014495 ? ? WWPDB D_1000014495 ? ? # 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 2002-08-09 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-07 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 4 'Structure model' 'Refinement description' 7 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' software 6 4 'Structure model' struct_site 7 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' '_struct_site.pdbx_auth_asym_id' 5 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1K2Z _pdbx_database_status.recvd_initial_deposition_date 2001-10-01 _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.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type NDB DD0042 'DD0042 is The Crystal Structure of d(GGCCAATTGG) Complexed with Distamycin.' unspecified NDB BD0006 'BD0006 is B-DNA at Atomic Resolution Reveals Extended Hydration Patterns.' unspecified NDB DD0002 'DD0002 is the Crystal Structure of d(GGCCAATTGG) Complexed with DAPI Reveals Novel Binding Mode.' unspecified NDB UDJ049 'UDJ049 is Parallel and Antiparallel (G.GC)2 Triple Helix Fragments in a Crystal Structure.' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Uytterhoeven, K.' 1 'Van Meervelt, L.' 2 # _citation.id primary _citation.title 'Two 1 : 1 binding modes for distamycin in the minor groove of d(GGCCAATTGG).' _citation.journal_abbrev Eur.J.Biochem. _citation.journal_volume 269 _citation.page_first 2868 _citation.page_last 2877 _citation.year 2002 _citation.journal_id_ASTM EJBCAI _citation.country IX _citation.journal_id_ISSN 0014-2956 _citation.journal_id_CSD 0262 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 12071949 _citation.pdbx_database_id_DOI 10.1046/j.1432-1033.2002.02952.x # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Uytterhoeven, K.' 1 ? primary 'Sponer, J.' 2 ? primary 'Van Meervelt, L.' 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(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3'" 3085.029 2 ? ? ? ? 2 non-polymer syn 'DISTAMYCIN A' 481.508 1 ? ? ? ? 3 water nat water 18.015 46 ? ? ? ? # _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)(DG)(DC)(DC)(DA)(DA)(DT)(DT)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can GGCCAATTGG _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 'DISTAMYCIN A' DMY 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 DG n 1 3 DC n 1 4 DC n 1 5 DA n 1 6 DA n 1 7 DT n 1 8 DT n 1 9 DG n 1 10 DG n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'This sequence is synthesized by Oswell DNA Service (Southampton, UK).' # 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 DMY non-polymer . 'DISTAMYCIN A' 'DISTAMYCIN; STALLIMYCIN' 'C22 H27 N9 O4' 481.508 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 DG 1 1 1 DG G A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DC 4 4 4 DC C A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DG 10 10 10 DG G A . n B 1 1 DG 1 11 11 DG G B . n B 1 2 DG 2 12 12 DG G B . n B 1 3 DC 3 13 13 DC C B . n B 1 4 DC 4 14 14 DC C B . n B 1 5 DA 5 15 15 DA A B . n B 1 6 DA 6 16 16 DA A B . n B 1 7 DT 7 17 17 DT T B . n B 1 8 DT 8 18 18 DT T B . n B 1 9 DG 9 19 19 DG G B . n B 1 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 2 DMY 1 21 -99999 DMY DMY A . D 3 HOH 1 22 -99999 HOH HOH A . D 3 HOH 2 23 -99999 HOH HOH A . D 3 HOH 3 25 -99999 HOH HOH A . D 3 HOH 4 28 -99999 HOH HOH A . D 3 HOH 5 31 -99999 HOH HOH A . D 3 HOH 6 33 -99999 HOH HOH A . D 3 HOH 7 34 -99999 HOH HOH A . D 3 HOH 8 35 -99999 HOH HOH A . D 3 HOH 9 36 -99999 HOH HOH A . D 3 HOH 10 39 -99999 HOH HOH A . D 3 HOH 11 41 -99999 HOH HOH A . D 3 HOH 12 43 -99999 HOH HOH A . D 3 HOH 13 44 -99999 HOH HOH A . D 3 HOH 14 46 -99999 HOH HOH A . D 3 HOH 15 51 -99999 HOH HOH A . D 3 HOH 16 52 -99999 HOH HOH A . D 3 HOH 17 54 -99999 HOH HOH A . D 3 HOH 18 56 -99999 HOH HOH A . D 3 HOH 19 57 -99999 HOH HOH A . D 3 HOH 20 61 -99999 HOH HOH A . D 3 HOH 21 63 -99999 HOH HOH A . D 3 HOH 22 64 -99999 HOH HOH A . D 3 HOH 23 66 -99999 HOH HOH A . D 3 HOH 24 67 -99999 HOH HOH A . E 3 HOH 1 24 -99999 HOH HOH B . E 3 HOH 2 26 -99999 HOH HOH B . E 3 HOH 3 27 -99999 HOH HOH B . E 3 HOH 4 29 -99999 HOH HOH B . E 3 HOH 5 30 -99999 HOH HOH B . E 3 HOH 6 32 -99999 HOH HOH B . E 3 HOH 7 37 -99999 HOH HOH B . E 3 HOH 8 38 -99999 HOH HOH B . E 3 HOH 9 40 -99999 HOH HOH B . E 3 HOH 10 42 -99999 HOH HOH B . E 3 HOH 11 45 -99999 HOH HOH B . E 3 HOH 12 47 -99999 HOH HOH B . E 3 HOH 13 48 -99999 HOH HOH B . E 3 HOH 14 49 -99999 HOH HOH B . E 3 HOH 15 50 -99999 HOH HOH B . E 3 HOH 16 53 -99999 HOH HOH B . E 3 HOH 17 55 -99999 HOH HOH B . E 3 HOH 18 58 -99999 HOH HOH B . E 3 HOH 19 59 -99999 HOH HOH B . E 3 HOH 20 60 -99999 HOH HOH B . E 3 HOH 21 62 -99999 HOH HOH B . E 3 HOH 22 65 -99999 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHELXL refinement . ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 # _cell.entry_id 1K2Z _cell.length_a 26.106 _cell.length_b 40.928 _cell.length_c 53.138 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1K2Z _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 # _exptl.entry_id 1K2Z _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.21 _exptl_crystal.density_percent_sol 44.31 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details 'MPD, magnesium chloride, cacodylate, spermine, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 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 MPD ? ? ? 1 2 1 MgCl2 ? ? ? 1 3 1 cacodylate ? ? ? 1 4 1 spermine ? ? ? 1 5 2 MPD ? ? ? 1 6 2 MgCl2 ? ? ? # _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 1999-04-09 _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 'Si 111' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9116 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'EMBL/DESY, HAMBURG BEAMLINE X11' _diffrn_source.pdbx_synchrotron_site 'EMBL/DESY, HAMBURG' _diffrn_source.pdbx_synchrotron_beamline X11 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9116 # _reflns.entry_id 1K2Z _reflns.observed_criterion_sigma_I 5.0 _reflns.observed_criterion_sigma_F 2.5 _reflns.d_resolution_low 50.0 _reflns.d_resolution_high 2.38 _reflns.number_obs 2351 _reflns.number_all 2538 _reflns.percent_possible_obs 92.7 _reflns.pdbx_Rmerge_I_obs 0.0410000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 22.60 _reflns.B_iso_Wilson_estimate 80.64 _reflns.pdbx_redundancy 5.5 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.38 _reflns_shell.d_res_low 2.42 _reflns_shell.percent_possible_all 93.4 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.2510000 _reflns_shell.meanI_over_sigI_obs 5.8 _reflns_shell.pdbx_redundancy 3.8 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 113 _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1K2Z _refine.ls_number_reflns_obs 2299 _refine.ls_number_reflns_all 2299 _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.ls_d_res_low 100.0 _refine.ls_d_res_high 2.38 _refine.ls_percent_reflns_obs 83.8 _refine.ls_R_factor_obs 0.2135000 _refine.ls_R_factor_all 0.2135000 _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean 72.9 _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model 'NDB entry DD0002' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model Isotropic _refine.pdbx_stereochemistry_target_values 'user defined' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R_Free ? _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.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_data_cutoff_high_rms_absF ? _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 410 _refine_hist.pdbx_number_atoms_ligand 35 _refine_hist.number_atoms_solvent 46 _refine_hist.number_atoms_total 491 _refine_hist.d_res_high 2.38 _refine_hist.d_res_low 100.0 # 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 0.02 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.05 ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 1K2Z _pdbx_refine.R_factor_all_no_cutoff 0.2135000 _pdbx_refine.R_factor_obs_no_cutoff 0.2135000 _pdbx_refine.free_R_factor_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff ? _pdbx_refine.free_R_val_test_set_ct_no_cutoff ? _pdbx_refine.R_factor_all_4sig_cutoff 0.2030000 _pdbx_refine.R_factor_obs_4sig_cutoff 0.2030000 _pdbx_refine.free_R_factor_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 83.8 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff ? _pdbx_refine.number_reflns_obs_4sig_cutoff 1928 _pdbx_refine.number_reflns_obs_no_cutoff 2299 _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _database_PDB_matrix.entry_id 1K2Z _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 1K2Z _struct.title 'The Crystal Structure of d(GGCCAATTGG) Complexed with Distamycin.' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1K2Z _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'B-DNA double helix, base triplets, minor groove binding, drug, distamycin, 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 1K2Z _struct_ref.pdbx_db_accession 1K2Z _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 1K2Z A 1 ? 10 ? 1K2Z 1 ? 10 ? 1 10 2 1 1K2Z B 1 ? 10 ? 1K2Z 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 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 3 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 3 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 3 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 4 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 4 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 4 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 4 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 5 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 9 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 9 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 9 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 DMY 21 ? 12 'BINDING SITE FOR RESIDUE DMY A 21' 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 12 DA A 5 ? DA A 5 . ? 1_555 ? 2 AC1 12 DA A 6 ? DA A 6 . ? 1_555 ? 3 AC1 12 DT A 7 ? DT A 7 . ? 1_555 ? 4 AC1 12 DT A 8 ? DT A 8 . ? 1_555 ? 5 AC1 12 DG A 9 ? DG A 9 . ? 1_555 ? 6 AC1 12 HOH D . ? HOH A 39 . ? 1_555 ? 7 AC1 12 DA B 5 ? DA B 15 . ? 1_555 ? 8 AC1 12 DA B 6 ? DA B 16 . ? 1_555 ? 9 AC1 12 DT B 7 ? DT B 17 . ? 1_555 ? 10 AC1 12 DT B 8 ? DT B 18 . ? 1_555 ? 11 AC1 12 DG B 9 ? DG B 19 . ? 1_555 ? 12 AC1 12 HOH E . ? HOH B 65 . ? 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 "C1'" A DC 3 ? ? N1 A DC 3 ? ? 1.572 1.488 0.084 0.013 N 2 1 "C1'" A DC 4 ? ? N1 A DC 4 ? ? 1.568 1.488 0.080 0.013 N 3 1 "C1'" A DA 5 ? ? N9 A DA 5 ? ? 1.371 1.468 -0.097 0.014 N 4 1 "C1'" A DA 6 ? ? N9 A DA 6 ? ? 1.368 1.468 -0.100 0.014 N 5 1 "C1'" B DC 13 ? ? N1 B DC 13 ? ? 1.568 1.488 0.080 0.013 N 6 1 "C1'" B DC 14 ? ? N1 B DC 14 ? ? 1.567 1.488 0.079 0.013 N 7 1 "C1'" B DA 15 ? ? N9 B DA 15 ? ? 1.371 1.468 -0.097 0.014 N 8 1 "C1'" B DA 16 ? ? N9 B DA 16 ? ? 1.374 1.468 -0.094 0.014 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 N9 A DG 1 ? ? "C1'" A DG 1 ? ? "C2'" A DG 1 ? ? 124.34 114.30 10.04 1.40 N 2 1 "O4'" A DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 94.48 108.00 -13.52 0.70 N 3 1 N9 A DG 2 ? ? "C1'" A DG 2 ? ? "C2'" A DG 2 ? ? 128.75 114.30 14.45 1.40 N 4 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 95.16 108.00 -12.84 0.70 N 5 1 "O4'" A DC 3 ? ? "C4'" A DC 3 ? ? "C3'" A DC 3 ? ? 110.53 106.00 4.53 0.60 N 6 1 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 102.89 108.00 -5.11 0.70 N 7 1 C6 A DC 3 ? ? N1 A DC 3 ? ? "C1'" A DC 3 ? ? 128.95 120.80 8.15 1.20 N 8 1 C2 A DC 3 ? ? N1 A DC 3 ? ? "C1'" A DC 3 ? ? 108.53 118.80 -10.27 1.10 N 9 1 C6 A DC 4 ? ? N1 A DC 4 ? ? "C1'" A DC 4 ? ? 132.00 120.80 11.20 1.20 N 10 1 C2 A DC 4 ? ? N1 A DC 4 ? ? "C1'" A DC 4 ? ? 107.93 118.80 -10.87 1.10 N 11 1 "O4'" A DA 5 ? ? "C1'" A DA 5 ? ? N9 A DA 5 ? ? 101.09 108.00 -6.91 0.70 N 12 1 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 99.86 108.00 -8.14 0.70 N 13 1 N1 A DT 7 ? ? "C1'" A DT 7 ? ? "C2'" A DT 7 ? ? 126.59 114.30 12.29 1.40 N 14 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 96.93 108.00 -11.07 0.70 N 15 1 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 118.78 122.90 -4.12 0.60 N 16 1 N1 A DT 8 ? ? "C1'" A DT 8 ? ? "C2'" A DT 8 ? ? 125.33 114.30 11.03 1.40 N 17 1 "O4'" A DT 8 ? ? "C1'" A DT 8 ? ? N1 A DT 8 ? ? 98.57 108.00 -9.43 0.70 N 18 1 N9 A DG 9 ? ? "C1'" A DG 9 ? ? "C2'" A DG 9 ? ? 123.08 114.30 8.78 1.40 N 19 1 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 94.95 108.00 -13.05 0.70 N 20 1 N9 A DG 10 ? ? "C1'" A DG 10 ? ? "C2'" A DG 10 ? ? 124.46 114.30 10.16 1.40 N 21 1 "O4'" A DG 10 ? ? "C1'" A DG 10 ? ? N9 A DG 10 ? ? 96.21 108.00 -11.79 0.70 N 22 1 N9 B DG 11 ? ? "C1'" B DG 11 ? ? "C2'" B DG 11 ? ? 123.50 114.30 9.20 1.40 N 23 1 "O4'" B DG 11 ? ? "C1'" B DG 11 ? ? N9 B DG 11 ? ? 95.71 108.00 -12.29 0.70 N 24 1 N9 B DG 12 ? ? "C1'" B DG 12 ? ? "C2'" B DG 12 ? ? 125.56 114.30 11.26 1.40 N 25 1 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? N9 B DG 12 ? ? 93.07 108.00 -14.93 0.70 N 26 1 C6 B DC 13 ? ? N1 B DC 13 ? ? "C1'" B DC 13 ? ? 132.25 120.80 11.45 1.20 N 27 1 C2 B DC 13 ? ? N1 B DC 13 ? ? "C1'" B DC 13 ? ? 107.39 118.80 -11.41 1.10 N 28 1 C6 B DC 14 ? ? N1 B DC 14 ? ? "C1'" B DC 14 ? ? 130.84 120.80 10.04 1.20 N 29 1 C2 B DC 14 ? ? N1 B DC 14 ? ? "C1'" B DC 14 ? ? 108.64 118.80 -10.16 1.10 N 30 1 "O4'" B DA 15 ? ? "C1'" B DA 15 ? ? N9 B DA 15 ? ? 100.36 108.00 -7.64 0.70 N 31 1 "O4'" B DA 16 ? ? "C1'" B DA 16 ? ? N9 B DA 16 ? ? 100.09 108.00 -7.91 0.70 N 32 1 N1 B DT 17 ? ? "C1'" B DT 17 ? ? "C2'" B DT 17 ? ? 126.64 114.30 12.34 1.40 N 33 1 "O4'" B DT 17 ? ? "C1'" B DT 17 ? ? N1 B DT 17 ? ? 98.61 108.00 -9.39 0.70 N 34 1 N1 B DT 18 ? ? "C1'" B DT 18 ? ? "C2'" B DT 18 ? ? 126.18 114.30 11.88 1.40 N 35 1 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 100.05 108.00 -7.95 0.70 N 36 1 N9 B DG 19 ? ? "C1'" B DG 19 ? ? "C2'" B DG 19 ? ? 124.53 114.30 10.23 1.40 N 37 1 "O4'" B DG 19 ? ? "C1'" B DG 19 ? ? N9 B DG 19 ? ? 94.90 108.00 -13.10 0.70 N 38 1 N9 B DG 20 ? ? "C1'" B DG 20 ? ? "C2'" B DG 20 ? ? 123.64 114.30 9.34 1.40 N 39 1 "O4'" B DG 20 ? ? "C1'" B DG 20 ? ? N9 B DG 20 ? ? 96.20 108.00 -11.80 0.70 N # _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 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 DMY C1 C N N 108 DMY O1 O N N 109 DMY N1 N N N 110 DMY C2 C Y N 111 DMY C3 C Y N 112 DMY C4 C Y N 113 DMY N2 N Y N 114 DMY C5 C Y N 115 DMY C6 C N N 116 DMY C7 C N N 117 DMY O2 O N N 118 DMY N3 N N N 119 DMY C8 C Y N 120 DMY C9 C Y N 121 DMY C10 C Y N 122 DMY N4 N Y N 123 DMY C11 C Y N 124 DMY C12 C N N 125 DMY C13 C N N 126 DMY O3 O N N 127 DMY N5 N N N 128 DMY C14 C Y N 129 DMY C15 C Y N 130 DMY C16 C Y N 131 DMY N6 N Y N 132 DMY C17 C Y N 133 DMY C18 C N N 134 DMY C19 C N N 135 DMY O4 O N N 136 DMY N7 N N N 137 DMY C20 C N N 138 DMY C21 C N N 139 DMY C22 C N N 140 DMY N8 N N N 141 DMY N9 N N N 142 DMY H1 H N N 143 DMY HN1 H N N 144 DMY H3 H N N 145 DMY H5 H N N 146 DMY H61 H N N 147 DMY H62 H N N 148 DMY H63 H N N 149 DMY HN3 H N N 150 DMY H9 H N N 151 DMY H11 H N N 152 DMY H121 H N N 153 DMY H122 H N N 154 DMY H123 H N N 155 DMY HN5 H N N 156 DMY H15 H N N 157 DMY H17 H N N 158 DMY H181 H N N 159 DMY H182 H N N 160 DMY H183 H N N 161 DMY HN7 H N N 162 DMY H201 H N N 163 DMY H202 H N N 164 DMY H211 H N N 165 DMY H212 H N N 166 DMY HN8 H N N 167 DMY HN91 H N N 168 DMY HN92 H N N 169 DT OP3 O N N 170 DT P P N N 171 DT OP1 O N N 172 DT OP2 O N N 173 DT "O5'" O N N 174 DT "C5'" C N N 175 DT "C4'" C N R 176 DT "O4'" O N N 177 DT "C3'" C N S 178 DT "O3'" O N N 179 DT "C2'" C N N 180 DT "C1'" C N R 181 DT N1 N N N 182 DT C2 C N N 183 DT O2 O N N 184 DT N3 N N N 185 DT C4 C N N 186 DT O4 O N N 187 DT C5 C N N 188 DT C7 C N N 189 DT C6 C N N 190 DT HOP3 H N N 191 DT HOP2 H N N 192 DT "H5'" H N N 193 DT "H5''" H N N 194 DT "H4'" H N N 195 DT "H3'" H N N 196 DT "HO3'" H N N 197 DT "H2'" H N N 198 DT "H2''" H N N 199 DT "H1'" H N N 200 DT H3 H N N 201 DT H71 H N N 202 DT H72 H N N 203 DT H73 H N N 204 DT H6 H N N 205 HOH O O N N 206 HOH H1 H N N 207 HOH H2 H N N 208 # 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 DMY C1 O1 doub N N 113 DMY C1 N1 sing N N 114 DMY C1 H1 sing N N 115 DMY N1 C2 sing N N 116 DMY N1 HN1 sing N N 117 DMY C2 C3 sing Y N 118 DMY C2 C5 doub Y N 119 DMY C3 C4 doub Y N 120 DMY C3 H3 sing N N 121 DMY C4 N2 sing Y N 122 DMY C4 C7 sing N N 123 DMY N2 C5 sing Y N 124 DMY N2 C6 sing N N 125 DMY C5 H5 sing N N 126 DMY C6 H61 sing N N 127 DMY C6 H62 sing N N 128 DMY C6 H63 sing N N 129 DMY C7 O2 doub N N 130 DMY C7 N3 sing N N 131 DMY N3 C8 sing N N 132 DMY N3 HN3 sing N N 133 DMY C8 C9 sing Y N 134 DMY C8 C11 doub Y N 135 DMY C9 C10 doub Y N 136 DMY C9 H9 sing N N 137 DMY C10 N4 sing Y N 138 DMY C10 C13 sing N N 139 DMY N4 C11 sing Y N 140 DMY N4 C12 sing N N 141 DMY C11 H11 sing N N 142 DMY C12 H121 sing N N 143 DMY C12 H122 sing N N 144 DMY C12 H123 sing N N 145 DMY C13 O3 doub N N 146 DMY C13 N5 sing N N 147 DMY N5 C14 sing N N 148 DMY N5 HN5 sing N N 149 DMY C14 C15 sing Y N 150 DMY C14 C17 doub Y N 151 DMY C15 C16 doub Y N 152 DMY C15 H15 sing N N 153 DMY C16 N6 sing Y N 154 DMY C16 C19 sing N N 155 DMY N6 C17 sing Y N 156 DMY N6 C18 sing N N 157 DMY C17 H17 sing N N 158 DMY C18 H181 sing N N 159 DMY C18 H182 sing N N 160 DMY C18 H183 sing N N 161 DMY C19 O4 doub N N 162 DMY C19 N7 sing N N 163 DMY N7 C20 sing N N 164 DMY N7 HN7 sing N N 165 DMY C20 C21 sing N N 166 DMY C20 H201 sing N N 167 DMY C20 H202 sing N N 168 DMY C21 C22 sing N N 169 DMY C21 H211 sing N N 170 DMY C21 H212 sing N N 171 DMY C22 N8 doub N N 172 DMY C22 N9 sing N N 173 DMY N8 HN8 sing N N 174 DMY N9 HN91 sing N N 175 DMY N9 HN92 sing N N 176 DT OP3 P sing N N 177 DT OP3 HOP3 sing N N 178 DT P OP1 doub N N 179 DT P OP2 sing N N 180 DT P "O5'" sing N N 181 DT OP2 HOP2 sing N N 182 DT "O5'" "C5'" sing N N 183 DT "C5'" "C4'" sing N N 184 DT "C5'" "H5'" sing N N 185 DT "C5'" "H5''" sing N N 186 DT "C4'" "O4'" sing N N 187 DT "C4'" "C3'" sing N N 188 DT "C4'" "H4'" sing N N 189 DT "O4'" "C1'" sing N N 190 DT "C3'" "O3'" sing N N 191 DT "C3'" "C2'" sing N N 192 DT "C3'" "H3'" sing N N 193 DT "O3'" "HO3'" sing N N 194 DT "C2'" "C1'" sing N N 195 DT "C2'" "H2'" sing N N 196 DT "C2'" "H2''" sing N N 197 DT "C1'" N1 sing N N 198 DT "C1'" "H1'" sing N N 199 DT N1 C2 sing N N 200 DT N1 C6 sing N N 201 DT C2 O2 doub N N 202 DT C2 N3 sing N N 203 DT N3 C4 sing N N 204 DT N3 H3 sing N N 205 DT C4 O4 doub N N 206 DT C4 C5 sing N N 207 DT C5 C7 sing N N 208 DT C5 C6 doub N N 209 DT C7 H71 sing N N 210 DT C7 H72 sing N N 211 DT C7 H73 sing N N 212 DT C6 H6 sing N N 213 HOH O H1 sing N N 214 HOH O H2 sing N N 215 # _ndb_struct_conf_na.entry_id 1K2Z _ndb_struct_conf_na.feature 'b-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 3 1_555 B DG 10 1_555 0.234 -0.493 -0.897 10.568 -6.662 -5.614 1 A_DC3:DG20_B A 3 ? B 20 ? 19 1 1 A DC 4 1_555 B DG 9 1_555 -0.622 -0.273 -0.442 9.073 2.601 -5.039 2 A_DC4:DG19_B A 4 ? B 19 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 0.378 -0.189 -0.108 7.079 -11.528 6.270 3 A_DA5:DT18_B A 5 ? B 18 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 0.432 -0.175 -0.098 7.965 -13.814 3.254 4 A_DA6:DT17_B A 6 ? B 17 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -1.124 -0.254 -0.321 2.308 -15.846 8.881 5 A_DT7:DA16_B A 7 ? B 16 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 0.043 -0.135 0.009 -6.039 -13.598 10.211 6 A_DT8:DA15_B A 8 ? B 15 ? 20 1 1 A DG 9 1_555 B DC 4 1_555 0.188 -0.095 -0.161 -6.903 -2.031 -4.047 7 A_DG9:DC14_B A 9 ? B 14 ? 19 1 1 A DG 10 1_555 B DC 3 1_555 0.057 0.023 0.048 -7.922 -11.602 -2.706 8 A_DG10:DC13_B A 10 ? B 13 ? 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 3 1_555 B DG 10 1_555 A DC 4 1_555 B DG 9 1_555 0.616 0.056 3.392 1.364 18.679 20.389 -4.691 -0.939 2.583 42.863 -3.130 27.618 1 AA_DC3DC4:DG19DG20_BB A 3 ? B 20 ? A 4 ? B 19 ? 1 A DC 4 1_555 B DG 9 1_555 A DA 5 1_555 B DT 8 1_555 0.530 0.589 3.351 1.115 7.738 48.363 0.101 -0.551 3.411 9.373 -1.351 48.953 2 AA_DC4DA5:DT18DG19_BB A 4 ? B 19 ? A 5 ? B 18 ? 1 A DA 5 1_555 B DT 8 1_555 A DA 6 1_555 B DT 7 1_555 -0.498 0.210 3.310 -3.263 -0.940 35.825 0.476 0.333 3.335 -1.524 5.289 35.981 3 AA_DA5DA6:DT17DT18_BB A 5 ? B 18 ? A 6 ? B 17 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 0.192 -0.704 3.326 3.734 -1.020 24.364 -1.328 0.721 3.343 -2.398 -8.776 24.665 4 AA_DA6DT7:DA16DT17_BB A 6 ? B 17 ? A 7 ? B 16 ? 1 A DT 7 1_555 B DA 6 1_555 A DT 8 1_555 B DA 5 1_555 0.713 0.494 3.375 1.024 3.599 44.519 0.308 -0.840 3.417 4.741 -1.349 44.668 5 AA_DT7DT8:DA15DA16_BB A 7 ? B 16 ? A 8 ? B 15 ? 1 A DT 8 1_555 B DA 5 1_555 A DG 9 1_555 B DC 4 1_555 -0.488 0.146 3.368 1.998 5.167 39.708 -0.395 0.946 3.333 7.562 -2.924 40.077 6 AA_DT8DG9:DC14DA15_BB A 8 ? B 15 ? A 9 ? B 14 ? 1 A DG 9 1_555 B DC 4 1_555 A DG 10 1_555 B DC 3 1_555 0.311 -0.241 3.266 -2.100 14.074 30.073 -2.744 -0.890 2.847 25.413 3.791 33.200 7 AA_DG9DG10:DC13DC14_BB A 9 ? B 14 ? A 10 ? B 13 ? # _pdbx_initial_refinement_model.accession_code 432D _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 DD0002' # _atom_sites.entry_id 1K2Z _atom_sites.fract_transf_matrix[1][1] 0.038305 _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] 0.024433 _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] 0.018819 _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 # loop_