data_2GB9 # _entry.id 2GB9 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 2GB9 pdb_00002gb9 10.2210/pdb2gb9/pdb NDB DD0078 ? ? RCSB RCSB036912 ? ? WWPDB D_1000036912 ? ? # 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 2006-04-25 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-18 5 'Structure model' 1 4 2024-02-14 # _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' Advisory 4 4 'Structure model' 'Refinement description' 5 5 'Structure model' 'Data collection' 6 5 'Structure model' 'Database references' 7 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' pdbx_unobs_or_zero_occ_atoms 2 4 'Structure model' software 3 5 'Structure model' chem_comp_atom 4 5 'Structure model' chem_comp_bond 5 5 'Structure model' database_2 6 5 'Structure model' pdbx_struct_conn_angle 7 5 'Structure model' struct_conn 8 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 4 'Structure model' '_software.name' 2 5 'Structure model' '_database_2.pdbx_DOI' 3 5 'Structure model' '_database_2.pdbx_database_accession' 4 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 6 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 7 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 8 5 'Structure model' '_pdbx_struct_conn_angle.value' 9 5 'Structure model' '_struct_conn.pdbx_dist_value' 10 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 11 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 12 5 'Structure model' '_struct_conn.ptnr2_symmetry' 13 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 14 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 15 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2GB9 _pdbx_database_status.recvd_initial_deposition_date 2006-03-10 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _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.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Hopcroft, N.H.' 1 'Brogden, A.L.' 2 'Searcey, M.' 3 'Cardin, C.J.' 4 # _citation.id primary _citation.title ;X-ray crystallographic study of DNA duplex cross-linking: simultaneous binding to two d(CGTACG)2 molecules by a bis(9-aminoacridine-4-carboxamide) derivative. ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 34 _citation.page_first 6663 _citation.page_last 6672 _citation.year 2006 _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 17145714 _citation.pdbx_database_id_DOI 10.1093/nar/gkl930 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Hopcroft, N.H.' 1 ? primary 'Brogden, A.L.' 2 ? primary 'Searcey, M.' 3 ? primary 'Cardin, C.J.' 4 ? # 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*GP*TP*AP*CP*G)-3'" 1809.217 2 ? ? ? ? 2 non-polymer syn 'STRONTIUM ION' 87.620 2 ? ? ? ? 3 non-polymer syn "9,9'-(HEXANE-1,6-DIYLDIIMINO)BIS{N-[2-(DIMETHYLAMINO)ETHYL]ACRIDINE-4-CARBOXAMIDE}" 698.899 2 ? ? ? ? 4 water nat water 18.015 103 ? ? ? ? # _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)(DG)(DT)(DA)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGTACG _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 'STRONTIUM ION' SR 3 "9,9'-(HEXANE-1,6-DIYLDIIMINO)BIS{N-[2-(DIMETHYLAMINO)ETHYL]ACRIDINE-4-CARBOXAMIDE}" A4C 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 DG n 1 3 DT n 1 4 DA n 1 5 DC n 1 6 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 A4C non-polymer . "9,9'-(HEXANE-1,6-DIYLDIIMINO)BIS{N-[2-(DIMETHYLAMINO)ETHYL]ACRIDINE-4-CARBOXAMIDE}" ? 'C42 H50 N8 O2' 698.899 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 SR non-polymer . 'STRONTIUM ION' ? 'Sr 2' 87.620 # 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 DG 2 2 2 DG G A . n A 1 3 DT 3 3 3 DT T A . n A 1 4 DA 4 4 4 DA A A . n A 1 5 DC 5 5 5 DC C A . n A 1 6 DG 6 6 6 DG G A . n B 1 1 DC 1 1 1 DC C B . n B 1 2 DG 2 2 2 DG G B . n B 1 3 DT 3 3 3 DT T B . n B 1 4 DA 4 4 4 DA A B . n B 1 5 DC 5 5 5 DC C B . n B 1 6 DG 6 6 6 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 SR 1 201 1 SR SR A . D 3 A4C 1 301 1 A4C DAC B . E 3 A4C 1 302 2 A4C DAC B . F 2 SR 1 202 2 SR SR B . G 4 HOH 1 202 3 HOH HOH A . G 4 HOH 2 203 5 HOH HOH A . G 4 HOH 3 204 8 HOH HOH A . G 4 HOH 4 205 10 HOH HOH A . G 4 HOH 5 206 11 HOH HOH A . G 4 HOH 6 207 12 HOH HOH A . G 4 HOH 7 208 14 HOH HOH A . G 4 HOH 8 209 15 HOH HOH A . G 4 HOH 9 210 17 HOH HOH A . G 4 HOH 10 211 18 HOH HOH A . G 4 HOH 11 212 22 HOH HOH A . G 4 HOH 12 213 27 HOH HOH A . G 4 HOH 13 214 29 HOH HOH A . G 4 HOH 14 215 31 HOH HOH A . G 4 HOH 15 216 32 HOH HOH A . G 4 HOH 16 217 33 HOH HOH A . G 4 HOH 17 218 37 HOH HOH A . G 4 HOH 18 219 38 HOH HOH A . G 4 HOH 19 220 39 HOH HOH A . G 4 HOH 20 221 40 HOH HOH A . G 4 HOH 21 222 42 HOH HOH A . G 4 HOH 22 223 43 HOH HOH A . G 4 HOH 23 224 50 HOH HOH A . G 4 HOH 24 225 51 HOH HOH A . G 4 HOH 25 226 52 HOH HOH A . G 4 HOH 26 227 56 HOH HOH A . G 4 HOH 27 228 59 HOH HOH A . G 4 HOH 28 229 61 HOH HOH A . G 4 HOH 29 230 63 HOH HOH A . G 4 HOH 30 231 65 HOH HOH A . G 4 HOH 31 232 66 HOH HOH A . G 4 HOH 32 233 67 HOH HOH A . G 4 HOH 33 234 70 HOH HOH A . G 4 HOH 34 235 71 HOH HOH A . G 4 HOH 35 236 72 HOH HOH A . G 4 HOH 36 237 78 HOH HOH A . G 4 HOH 37 238 81 HOH HOH A . G 4 HOH 38 239 85 HOH HOH A . G 4 HOH 39 240 86 HOH HOH A . G 4 HOH 40 241 87 HOH HOH A . G 4 HOH 41 242 88 HOH HOH A . G 4 HOH 42 243 89 HOH HOH A . G 4 HOH 43 244 92 HOH HOH A . G 4 HOH 44 245 93 HOH HOH A . G 4 HOH 45 246 94 HOH HOH A . G 4 HOH 46 247 99 HOH HOH A . G 4 HOH 47 248 100 HOH HOH A . G 4 HOH 48 249 103 HOH HOH A . H 4 HOH 1 303 1 HOH HOH B . H 4 HOH 2 304 2 HOH HOH B . H 4 HOH 3 305 4 HOH HOH B . H 4 HOH 4 306 6 HOH HOH B . H 4 HOH 5 307 7 HOH HOH B . H 4 HOH 6 308 9 HOH HOH B . H 4 HOH 7 309 13 HOH HOH B . H 4 HOH 8 310 16 HOH HOH B . H 4 HOH 9 311 19 HOH HOH B . H 4 HOH 10 312 20 HOH HOH B . H 4 HOH 11 313 21 HOH HOH B . H 4 HOH 12 314 23 HOH HOH B . H 4 HOH 13 315 24 HOH HOH B . H 4 HOH 14 316 25 HOH HOH B . H 4 HOH 15 317 26 HOH HOH B . H 4 HOH 16 318 28 HOH HOH B . H 4 HOH 17 319 30 HOH HOH B . H 4 HOH 18 320 34 HOH HOH B . H 4 HOH 19 321 35 HOH HOH B . H 4 HOH 20 322 36 HOH HOH B . H 4 HOH 21 323 41 HOH HOH B . H 4 HOH 22 324 44 HOH HOH B . H 4 HOH 23 325 45 HOH HOH B . H 4 HOH 24 326 46 HOH HOH B . H 4 HOH 25 327 47 HOH HOH B . H 4 HOH 26 328 48 HOH HOH B . H 4 HOH 27 329 49 HOH HOH B . H 4 HOH 28 330 53 HOH HOH B . H 4 HOH 29 331 54 HOH HOH B . H 4 HOH 30 332 55 HOH HOH B . H 4 HOH 31 333 57 HOH HOH B . H 4 HOH 32 334 58 HOH HOH B . H 4 HOH 33 335 60 HOH HOH B . H 4 HOH 34 336 62 HOH HOH B . H 4 HOH 35 337 64 HOH HOH B . H 4 HOH 36 338 68 HOH HOH B . H 4 HOH 37 339 69 HOH HOH B . H 4 HOH 38 340 73 HOH HOH B . H 4 HOH 39 341 74 HOH HOH B . H 4 HOH 40 342 75 HOH HOH B . H 4 HOH 41 343 76 HOH HOH B . H 4 HOH 42 344 77 HOH HOH B . H 4 HOH 43 345 79 HOH HOH B . H 4 HOH 44 346 80 HOH HOH B . H 4 HOH 45 347 82 HOH HOH B . H 4 HOH 46 348 83 HOH HOH B . H 4 HOH 47 349 84 HOH HOH B . H 4 HOH 48 350 90 HOH HOH B . H 4 HOH 49 351 91 HOH HOH B . H 4 HOH 50 352 95 HOH HOH B . H 4 HOH 51 353 96 HOH HOH B . H 4 HOH 52 354 97 HOH HOH B . H 4 HOH 53 355 98 HOH HOH B . H 4 HOH 54 356 101 HOH HOH B . H 4 HOH 55 357 102 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 SCALEPACK 'data scaling' . ? 2 HKL2Map 'model building' . ? 3 SHELXL-97 refinement . ? 4 HKL2Map phasing . ? 5 # _cell.entry_id 2GB9 _cell.length_a 37.210 _cell.length_b 37.210 _cell.length_c 53.480 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 2GB9 _symmetry.space_group_name_H-M 'P 43 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 95 _symmetry.space_group_name_Hall ? # _exptl.entry_id 2GB9 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.35 _exptl_crystal.density_percent_sol 47.6 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details 'SODIUM CACODYLATE pH7.0, SrCl2, SPERMINE, MPD, SITTING DROP VAPOUR DIFFUSION AT 291K, VAPOR DIFFUSION, SITTING DROP' _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 SrCl2 ? ? ? 1 3 1 SPERMINE ? ? ? 1 4 1 MPD ? ? ? 1 5 1 H2O ? ? ? 1 6 2 'SODIUM CACODYLATE' ? ? ? 1 7 2 SrCl2 ? ? ? 1 8 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2005-09-02 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.769 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE BM14' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline BM14 _diffrn_source.pdbx_wavelength 0.769 _diffrn_source.pdbx_wavelength_list 0.769 # _reflns.entry_id 2GB9 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 37.2 _reflns.d_resolution_high 1.70 _reflns.number_obs 4509 _reflns.number_all 4509 _reflns.percent_possible_obs 100.0 _reflns.pdbx_Rmerge_I_obs 0.064 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 4.2 _reflns.B_iso_Wilson_estimate 16.2 _reflns.pdbx_redundancy 26.8 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.70 _reflns_shell.d_res_low 1.79 _reflns_shell.percent_possible_all 100.0 _reflns_shell.Rmerge_I_obs 0.204 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.4 _reflns_shell.pdbx_redundancy 27.9 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 626 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 2GB9 _refine.ls_number_reflns_obs 4204 _refine.ls_number_reflns_all 4204 _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 8.00 _refine.ls_d_res_high 1.70 _refine.ls_percent_reflns_obs 95.0 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.213 _refine.ls_R_factor_R_free 0.2544 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.0 _refine.ls_number_reflns_R_free 221 _refine.ls_number_parameters 1589 _refine.ls_number_restraints 1895 _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method 'FREE R' _refine.details 'ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'ENGH AND HUBER' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_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_analyze.entry_id 2GB9 _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues 0 _refine_analyze.occupancy_sum_hydrogen 0.00 _refine_analyze.occupancy_sum_non_hydrogen 393.00 _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 240 _refine_hist.pdbx_number_atoms_ligand 54 _refine_hist.number_atoms_solvent 103 _refine_hist.number_atoms_total 397 _refine_hist.d_res_high 1.70 _refine_hist.d_res_low 8.00 # 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 0.026 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.021 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes 0.0045 ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr 0.012 ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt 0.063 ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps 0.000 ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 2GB9 _pdbx_refine.R_factor_all_no_cutoff ? _pdbx_refine.R_factor_obs_no_cutoff 0.213 _pdbx_refine.free_R_factor_no_cutoff 0.2544 _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 5.0 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 221 _pdbx_refine.R_factor_all_4sig_cutoff ? _pdbx_refine.R_factor_obs_4sig_cutoff ? _pdbx_refine.free_R_factor_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff ? _pdbx_refine.number_reflns_obs_4sig_cutoff ? _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _database_PDB_matrix.entry_id 2GB9 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.000000 _database_PDB_matrix.origx_vector[2] 0.000000 _database_PDB_matrix.origx_vector[3] 0.000000 # _struct.entry_id 2GB9 _struct.title 'd(CGTACG)2 crosslinked bis-acridine complex' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2GB9 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA DUPLEX CROSSLINKING, 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 ? F N N 2 ? G N N 4 ? H N N 4 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2GB9 _struct_ref.pdbx_db_accession 2GB9 _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 2GB9 A 1 ? 6 ? 2GB9 1 ? 6 ? 1 6 2 1 2GB9 B 1 ? 6 ? 2GB9 1 ? 6 ? 1 6 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 5_655 -x+1,y,-z -1.0000000000 0.0000000000 0.0000000000 37.2100000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 3 'crystal symmetry operation' 6_565 x,-y+1,-z+1/2 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 37.2100000000 0.0000000000 0.0000000000 -1.0000000000 26.7400000000 # _struct_biol.id 1 _struct_biol.details ;The other halves of the two drugs in the asymmetric unit are generated by the symmetry operations (1-x,y,-z) and (x,1-y,-z+0.5) respectively. ; _struct_biol.pdbx_parent_biol_id ? # 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 covale1 covale none ? D A4C . CX3 ? ? ? 1_555 D A4C . CX3 ? ? B A4C 301 B A4C 301 5_655 ? ? ? ? ? ? ? 1.527 ? ? covale2 covale none ? E A4C . CX3 ? ? ? 1_555 E A4C . CX3 ? ? B A4C 302 B A4C 302 6_565 ? ? ? ? ? ? ? 1.513 ? ? metalc1 metalc ? ? C SR . SR ? ? ? 1_555 G HOH . O ? ? A SR 201 A HOH 227 1_555 ? ? ? ? ? ? ? 2.853 ? ? metalc2 metalc ? ? C SR . SR ? ? ? 1_555 G HOH . O ? ? A SR 201 A HOH 235 1_555 ? ? ? ? ? ? ? 2.840 ? ? metalc3 metalc ? ? C SR . SR ? ? ? 1_555 H HOH . O ? ? A SR 201 B HOH 313 1_555 ? ? ? ? ? ? ? 2.623 ? ? metalc4 metalc ? ? C SR . SR ? ? ? 1_555 H HOH . O ? ? A SR 201 B HOH 315 1_555 ? ? ? ? ? ? ? 2.486 ? ? metalc5 metalc ? ? C SR . SR ? ? ? 1_555 H HOH . O ? ? A SR 201 B HOH 333 1_555 ? ? ? ? ? ? ? 2.678 ? ? metalc6 metalc ? ? C SR . SR ? ? ? 1_555 H HOH . O ? ? A SR 201 B HOH 356 1_555 ? ? ? ? ? ? ? 2.840 ? ? metalc7 metalc ? ? F SR . SR ? ? ? 1_555 H HOH . O ? ? B SR 202 B HOH 316 1_555 ? ? ? ? ? ? ? 2.651 ? ? metalc8 metalc ? ? F SR . SR ? ? ? 1_555 H HOH . O ? ? B SR 202 B HOH 316 8_664 ? ? ? ? ? ? ? 2.651 ? ? metalc9 metalc ? ? F SR . SR ? ? ? 1_555 H HOH . O ? ? B SR 202 B HOH 349 1_555 ? ? ? ? ? ? ? 2.211 ? ? metalc10 metalc ? ? F SR . SR ? ? ? 1_555 H HOH . O ? ? B SR 202 B HOH 349 8_664 ? ? ? ? ? ? ? 2.211 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 1 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 1 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 1 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 2 B DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 2 B DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 2 B DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 3 B DA 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 3 B DA 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 3 N3 ? ? A DA 4 B DT 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 4 B DT 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 5 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 5 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 5 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 6 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 6 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 6 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? G HOH . ? A HOH 227 ? 1_555 SR ? C SR . ? A SR 201 ? 1_555 O ? G HOH . ? A HOH 235 ? 1_555 64.8 ? 2 O ? G HOH . ? A HOH 227 ? 1_555 SR ? C SR . ? A SR 201 ? 1_555 O ? H HOH . ? B HOH 313 ? 1_555 149.5 ? 3 O ? G HOH . ? A HOH 235 ? 1_555 SR ? C SR . ? A SR 201 ? 1_555 O ? H HOH . ? B HOH 313 ? 1_555 139.6 ? 4 O ? G HOH . ? A HOH 227 ? 1_555 SR ? C SR . ? A SR 201 ? 1_555 O ? H HOH . ? B HOH 315 ? 1_555 142.3 ? 5 O ? G HOH . ? A HOH 235 ? 1_555 SR ? C SR . ? A SR 201 ? 1_555 O ? H HOH . ? B HOH 315 ? 1_555 82.4 ? 6 O ? H HOH . ? B HOH 313 ? 1_555 SR ? C SR . ? A SR 201 ? 1_555 O ? H HOH . ? B HOH 315 ? 1_555 68.2 ? 7 O ? G HOH . ? A HOH 227 ? 1_555 SR ? C SR . ? A SR 201 ? 1_555 O ? H HOH . ? B HOH 333 ? 1_555 95.1 ? 8 O ? G HOH . ? A HOH 235 ? 1_555 SR ? C SR . ? A SR 201 ? 1_555 O ? H HOH . ? B HOH 333 ? 1_555 155.1 ? 9 O ? H HOH . ? B HOH 313 ? 1_555 SR ? C SR . ? A SR 201 ? 1_555 O ? H HOH . ? B HOH 333 ? 1_555 64.8 ? 10 O ? H HOH . ? B HOH 315 ? 1_555 SR ? C SR . ? A SR 201 ? 1_555 O ? H HOH . ? B HOH 333 ? 1_555 110.1 ? 11 O ? G HOH . ? A HOH 227 ? 1_555 SR ? C SR . ? A SR 201 ? 1_555 O ? H HOH . ? B HOH 356 ? 1_555 88.4 ? 12 O ? G HOH . ? A HOH 235 ? 1_555 SR ? C SR . ? A SR 201 ? 1_555 O ? H HOH . ? B HOH 356 ? 1_555 57.5 ? 13 O ? H HOH . ? B HOH 313 ? 1_555 SR ? C SR . ? A SR 201 ? 1_555 O ? H HOH . ? B HOH 356 ? 1_555 119.4 ? 14 O ? H HOH . ? B HOH 315 ? 1_555 SR ? C SR . ? A SR 201 ? 1_555 O ? H HOH . ? B HOH 356 ? 1_555 57.2 ? 15 O ? H HOH . ? B HOH 333 ? 1_555 SR ? C SR . ? A SR 201 ? 1_555 O ? H HOH . ? B HOH 356 ? 1_555 110.3 ? 16 O ? H HOH . ? B HOH 316 ? 1_555 SR ? F SR . ? B SR 202 ? 1_555 O ? H HOH . ? B HOH 316 ? 8_664 152.4 ? 17 O ? H HOH . ? B HOH 316 ? 1_555 SR ? F SR . ? B SR 202 ? 1_555 O ? H HOH . ? B HOH 349 ? 1_555 89.3 ? 18 O ? H HOH . ? B HOH 316 ? 8_664 SR ? F SR . ? B SR 202 ? 1_555 O ? H HOH . ? B HOH 349 ? 1_555 80.4 ? 19 O ? H HOH . ? B HOH 316 ? 1_555 SR ? F SR . ? B SR 202 ? 1_555 O ? H HOH . ? B HOH 349 ? 8_664 80.4 ? 20 O ? H HOH . ? B HOH 316 ? 8_664 SR ? F SR . ? B SR 202 ? 1_555 O ? H HOH . ? B HOH 349 ? 8_664 89.3 ? 21 O ? H HOH . ? B HOH 349 ? 1_555 SR ? F SR . ? B SR 202 ? 1_555 O ? H HOH . ? B HOH 349 ? 8_664 136.2 ? # 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 B A4C 301 ? 7 'BINDING SITE FOR RESIDUE A4C B 301' AC2 Software B A4C 302 ? 9 'BINDING SITE FOR RESIDUE A4C B 302' AC3 Software A SR 201 ? 6 'BINDING SITE FOR RESIDUE SR A 201' AC4 Software B SR 202 ? 4 'BINDING SITE FOR RESIDUE SR B 202' 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 7 DC A 5 ? DC A 5 . ? 1_555 ? 2 AC1 7 DG A 6 ? DG A 6 . ? 1_555 ? 3 AC1 7 DC B 1 ? DC B 1 . ? 1_555 ? 4 AC1 7 DG B 2 ? DG B 2 . ? 1_555 ? 5 AC1 7 DT B 3 ? DT B 3 . ? 1_555 ? 6 AC1 7 HOH H . ? HOH B 304 . ? 1_555 ? 7 AC1 7 HOH H . ? HOH B 342 . ? 1_555 ? 8 AC2 9 DC A 1 ? DC A 1 . ? 1_555 ? 9 AC2 9 DG A 2 ? DG A 2 . ? 1_555 ? 10 AC2 9 DG A 2 ? DG A 2 . ? 6_565 ? 11 AC2 9 DG A 6 ? DG A 6 . ? 7_655 ? 12 AC2 9 HOH G . ? HOH A 229 . ? 7_655 ? 13 AC2 9 DC B 5 ? DC B 5 . ? 1_555 ? 14 AC2 9 DG B 6 ? DG B 6 . ? 1_555 ? 15 AC2 9 HOH H . ? HOH B 317 . ? 1_555 ? 16 AC2 9 HOH H . ? HOH B 321 . ? 1_555 ? 17 AC3 6 HOH G . ? HOH A 227 . ? 1_555 ? 18 AC3 6 HOH G . ? HOH A 235 . ? 1_555 ? 19 AC3 6 HOH H . ? HOH B 313 . ? 1_555 ? 20 AC3 6 HOH H . ? HOH B 315 . ? 1_555 ? 21 AC3 6 HOH H . ? HOH B 333 . ? 1_555 ? 22 AC3 6 HOH H . ? HOH B 356 . ? 1_555 ? 23 AC4 4 HOH H . ? HOH B 316 . ? 8_664 ? 24 AC4 4 HOH H . ? HOH B 316 . ? 1_555 ? 25 AC4 4 HOH H . ? HOH B 349 . ? 1_555 ? 26 AC4 4 HOH H . ? HOH B 349 . ? 8_664 ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? 1.503 1.420 0.083 0.011 N 2 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? 1.492 1.420 0.072 0.011 N 3 1 "C5'" A DC 5 ? ? "C4'" A DC 5 ? ? 1.558 1.512 0.046 0.007 N 4 1 "C1'" A DG 6 ? ? N9 A DG 6 ? ? 1.571 1.488 0.083 0.013 N 5 1 C6 A DG 6 ? ? N1 A DG 6 ? ? 1.433 1.391 0.042 0.007 N 6 1 "O4'" B DC 1 ? ? "C1'" B DC 1 ? ? 1.490 1.420 0.070 0.011 N 7 1 "C1'" B DG 2 ? ? N9 B DG 2 ? ? 1.571 1.488 0.083 0.013 N 8 1 "C5'" B DG 6 ? ? "C4'" B DG 6 ? ? 1.571 1.512 0.059 0.007 N 9 1 "C1'" B DG 6 ? ? N9 B DG 6 ? ? 1.570 1.488 0.082 0.013 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 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 101.30 108.00 -6.70 0.70 N 2 1 C2 A DG 2 ? ? N3 A DG 2 ? ? C4 A DG 2 ? ? 108.82 111.90 -3.08 0.50 N 3 1 N1 A DT 3 ? ? "C1'" A DT 3 ? ? "C2'" A DT 3 ? ? 123.69 114.30 9.39 1.40 N 4 1 C6 A DT 3 ? ? N1 A DT 3 ? ? C2 A DT 3 ? ? 124.76 121.30 3.46 0.50 N 5 1 N3 A DT 3 ? ? C2 A DT 3 ? ? O2 A DT 3 ? ? 126.88 122.30 4.58 0.60 N 6 1 C4 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 123.20 119.00 4.20 0.60 N 7 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 99.66 108.00 -8.34 0.70 N 8 1 OP1 A DC 5 ? ? P A DC 5 ? ? OP2 A DC 5 ? ? 129.19 119.60 9.59 1.50 N 9 1 N1 A DC 5 ? ? "C1'" A DC 5 ? ? "C2'" A DC 5 ? ? 126.29 114.30 11.99 1.40 N 10 1 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 120.28 108.30 11.98 0.30 N 11 1 C6 A DC 5 ? ? N1 A DC 5 ? ? "C1'" A DC 5 ? ? 113.08 120.80 -7.72 1.20 N 12 1 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 96.42 108.00 -11.58 0.70 N 13 1 N1 A DG 6 ? ? C6 A DG 6 ? ? O6 A DG 6 ? ? 115.88 119.90 -4.02 0.60 N 14 1 C5 A DG 6 ? ? C6 A DG 6 ? ? O6 A DG 6 ? ? 132.81 128.60 4.21 0.60 N 15 1 N1 B DC 1 ? ? "C1'" B DC 1 ? ? "C2'" B DC 1 ? ? 127.16 114.30 12.86 1.40 N 16 1 C6 B DC 1 ? ? N1 B DC 1 ? ? C2 B DC 1 ? ? 125.17 120.30 4.87 0.40 N 17 1 N3 B DC 1 ? ? C4 B DC 1 ? ? C5 B DC 1 ? ? 124.44 121.90 2.54 0.40 N 18 1 "O4'" B DG 2 ? ? "C1'" B DG 2 ? ? N9 B DG 2 ? ? 97.62 108.00 -10.38 0.70 N 19 1 N1 B DT 3 ? ? "C1'" B DT 3 ? ? "C2'" B DT 3 ? ? 133.13 114.30 18.83 1.40 N 20 1 "O4'" B DT 3 ? ? "C1'" B DT 3 ? ? N1 B DT 3 ? ? 103.32 108.00 -4.68 0.70 N 21 1 C6 B DT 3 ? ? N1 B DT 3 ? ? C2 B DT 3 ? ? 118.13 121.30 -3.17 0.50 N 22 1 C2 B DT 3 ? ? N3 B DT 3 ? ? C4 B DT 3 ? ? 131.36 127.20 4.16 0.60 N 23 1 N3 B DT 3 ? ? C4 B DT 3 ? ? C5 B DT 3 ? ? 111.30 115.20 -3.90 0.60 N 24 1 N1 B DT 3 ? ? C2 B DT 3 ? ? O2 B DT 3 ? ? 116.34 123.10 -6.76 0.80 N 25 1 N3 B DT 3 ? ? C2 B DT 3 ? ? O2 B DT 3 ? ? 129.45 122.30 7.15 0.60 N 26 1 N3 B DT 3 ? ? C4 B DT 3 ? ? O4 B DT 3 ? ? 125.24 119.90 5.34 0.60 N 27 1 "O4'" B DC 5 ? ? "C1'" B DC 5 ? ? N1 B DC 5 ? ? 111.13 108.30 2.83 0.30 N 28 1 "O4'" B DG 6 ? ? "C1'" B DG 6 ? ? N9 B DG 6 ? ? 102.30 108.00 -5.70 0.70 N # _struct_site_keywords.site_id 1 _struct_site_keywords.text bis-intercalation # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 B SR 202 ? F SR . 2 1 A HOH 207 ? G HOH . 3 1 B HOH 334 ? H HOH . 4 1 B HOH 345 ? H HOH . 5 1 B HOH 357 ? H HOH . # _pdbx_database_remark.id 600 _pdbx_database_remark.text ;HETEROGEN A4C 301 AND A4C 302 REPRESENT TWO CRYSTALLOGRAPHICALLY DISTINCT COPIES OF THE LIGAND. EACH OF THESE TWO MOLECULES LIES ON A CRYSTALLOGRAPHIC AXIS OF TWO-FOLD ROTATIONAL SYMMETRY. HENCE, IN BOTH CASES, ONLY HALF OF THE LIGAND IS PRESENT IN THE COORDINATE FILE SUBMITTED, WHICH CORRESPONDS TO ONE ASYMMETRIC UNIT. THE OTHER HALF OF EACH LIGAND CAN BE GENERATED THROUGH SYMMETRY. LINKS ARE PROVIDED BETWEEN SYMMETRY RELATED CX3 ATOMS. ; # 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 A4C OD1 O N N 1 A4C CD1 C N N 2 A4C ND1 N N N 3 A4C CD2 C N N 4 A4C CD3 C N N 5 A4C ND2 N N N 6 A4C CD8 C N N 7 A4C CD7 C N N 8 A4C C4 C Y N 9 A4C C3 C Y N 10 A4C C2 C Y N 11 A4C C12 C Y N 12 A4C C11 C Y N 13 A4C C1 C Y N 14 A4C N10 N Y N 15 A4C C14 C Y N 16 A4C C5 C Y N 17 A4C C6 C Y N 18 A4C C7 C Y N 19 A4C C13 C Y N 20 A4C C8 C Y N 21 A4C C9 C Y N 22 A4C N9 N N N 23 A4C CX1 C N N 24 A4C CX2 C N N 25 A4C CX3 C N N 26 A4C OD2 O N N 27 A4C CD4 C N N 28 A4C ND3 N N N 29 A4C CD5 C N N 30 A4C CD6 C N N 31 A4C ND4 N N N 32 A4C CD0 C N N 33 A4C CD9 C N N 34 A4C C25 C Y N 35 A4C C26 C Y N 36 A4C C15 C Y N 37 A4C C27 C Y N 38 A4C C16 C Y N 39 A4C C17 C Y N 40 A4C N12 N Y N 41 A4C C18 C Y N 42 A4C C19 C Y N 43 A4C C20 C Y N 44 A4C C21 C Y N 45 A4C C22 C Y N 46 A4C C23 C Y N 47 A4C C24 C Y N 48 A4C N11 N N N 49 A4C CX4 C N N 50 A4C CX5 C N N 51 A4C CX6 C N N 52 A4C HND1 H N N 53 A4C HD21 H N N 54 A4C HD22 H N N 55 A4C HD31 H N N 56 A4C HD32 H N N 57 A4C HD81 H N N 58 A4C HD82 H N N 59 A4C HD83 H N N 60 A4C HD71 H N N 61 A4C HD72 H N N 62 A4C HD73 H N N 63 A4C H3 H N N 64 A4C H2 H N N 65 A4C H1 H N N 66 A4C H5 H N N 67 A4C H6 H N N 68 A4C H7 H N N 69 A4C H8 H N N 70 A4C HN9 H N N 71 A4C HX11 H N N 72 A4C HX12 H N N 73 A4C HX21 H N N 74 A4C HX22 H N N 75 A4C HX31 H N N 76 A4C HX32 H N N 77 A4C HND3 H N N 78 A4C HD51 H N N 79 A4C HD52 H N N 80 A4C HD61 H N N 81 A4C HD62 H N N 82 A4C HD01 H N N 83 A4C HD02 H N N 84 A4C HD03 H N N 85 A4C HD91 H N N 86 A4C HD92 H N N 87 A4C HD93 H N N 88 A4C H26 H N N 89 A4C H15 H N N 90 A4C H17 H N N 91 A4C H19 H N N 92 A4C H20 H N N 93 A4C H21 H N N 94 A4C H23 H N N 95 A4C HN11 H N N 96 A4C HX41 H N N 97 A4C HX42 H N N 98 A4C HX51 H N N 99 A4C HX52 H N N 100 A4C HX61 H N N 101 A4C HX62 H N N 102 DA OP3 O N N 103 DA P P N N 104 DA OP1 O N N 105 DA OP2 O N N 106 DA "O5'" O N N 107 DA "C5'" C N N 108 DA "C4'" C N R 109 DA "O4'" O N N 110 DA "C3'" C N S 111 DA "O3'" O N N 112 DA "C2'" C N N 113 DA "C1'" C N R 114 DA N9 N Y N 115 DA C8 C Y N 116 DA N7 N Y N 117 DA C5 C Y N 118 DA C6 C Y N 119 DA N6 N N N 120 DA N1 N Y N 121 DA C2 C Y N 122 DA N3 N Y N 123 DA C4 C Y N 124 DA HOP3 H N N 125 DA HOP2 H N N 126 DA "H5'" H N N 127 DA "H5''" H N N 128 DA "H4'" H N N 129 DA "H3'" H N N 130 DA "HO3'" H N N 131 DA "H2'" H N N 132 DA "H2''" H N N 133 DA "H1'" H N N 134 DA H8 H N N 135 DA H61 H N N 136 DA H62 H N N 137 DA H2 H N N 138 DC OP3 O N N 139 DC P P N N 140 DC OP1 O N N 141 DC OP2 O N N 142 DC "O5'" O N N 143 DC "C5'" C N N 144 DC "C4'" C N R 145 DC "O4'" O N N 146 DC "C3'" C N S 147 DC "O3'" O N N 148 DC "C2'" C N N 149 DC "C1'" C N R 150 DC N1 N N N 151 DC C2 C N N 152 DC O2 O N N 153 DC N3 N N N 154 DC C4 C N N 155 DC N4 N N N 156 DC C5 C N N 157 DC C6 C N N 158 DC HOP3 H N N 159 DC HOP2 H N N 160 DC "H5'" H N N 161 DC "H5''" H N N 162 DC "H4'" H N N 163 DC "H3'" H N N 164 DC "HO3'" H N N 165 DC "H2'" H N N 166 DC "H2''" H N N 167 DC "H1'" H N N 168 DC H41 H N N 169 DC H42 H N N 170 DC H5 H N N 171 DC H6 H N N 172 DG OP3 O N N 173 DG P P N N 174 DG OP1 O N N 175 DG OP2 O N N 176 DG "O5'" O N N 177 DG "C5'" C N N 178 DG "C4'" C N R 179 DG "O4'" O N N 180 DG "C3'" C N S 181 DG "O3'" O N N 182 DG "C2'" C N N 183 DG "C1'" C N R 184 DG N9 N Y N 185 DG C8 C Y N 186 DG N7 N Y N 187 DG C5 C Y N 188 DG C6 C N N 189 DG O6 O N N 190 DG N1 N N N 191 DG C2 C N N 192 DG N2 N N N 193 DG N3 N N N 194 DG C4 C Y N 195 DG HOP3 H N N 196 DG HOP2 H N N 197 DG "H5'" H N N 198 DG "H5''" H N N 199 DG "H4'" H N N 200 DG "H3'" H N N 201 DG "HO3'" H N N 202 DG "H2'" H N N 203 DG "H2''" H N N 204 DG "H1'" H N N 205 DG H8 H N N 206 DG H1 H N N 207 DG H21 H N N 208 DG H22 H N N 209 DT OP3 O N N 210 DT P P N N 211 DT OP1 O N N 212 DT OP2 O N N 213 DT "O5'" O N N 214 DT "C5'" C N N 215 DT "C4'" C N R 216 DT "O4'" O N N 217 DT "C3'" C N S 218 DT "O3'" O N N 219 DT "C2'" C N N 220 DT "C1'" C N R 221 DT N1 N N N 222 DT C2 C N N 223 DT O2 O N N 224 DT N3 N N N 225 DT C4 C N N 226 DT O4 O N N 227 DT C5 C N N 228 DT C7 C N N 229 DT C6 C N N 230 DT HOP3 H N N 231 DT HOP2 H N N 232 DT "H5'" H N N 233 DT "H5''" H N N 234 DT "H4'" H N N 235 DT "H3'" H N N 236 DT "HO3'" H N N 237 DT "H2'" H N N 238 DT "H2''" H N N 239 DT "H1'" H N N 240 DT H3 H N N 241 DT H71 H N N 242 DT H72 H N N 243 DT H73 H N N 244 DT H6 H N N 245 HOH O O N N 246 HOH H1 H N N 247 HOH H2 H N N 248 SR SR SR N N 249 # 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 A4C OD1 CD1 doub N N 1 A4C CD1 ND1 sing N N 2 A4C CD1 C4 sing N N 3 A4C ND1 CD2 sing N N 4 A4C ND1 HND1 sing N N 5 A4C CD2 CD3 sing N N 6 A4C CD2 HD21 sing N N 7 A4C CD2 HD22 sing N N 8 A4C CD3 ND2 sing N N 9 A4C CD3 HD31 sing N N 10 A4C CD3 HD32 sing N N 11 A4C ND2 CD8 sing N N 12 A4C ND2 CD7 sing N N 13 A4C CD8 HD81 sing N N 14 A4C CD8 HD82 sing N N 15 A4C CD8 HD83 sing N N 16 A4C CD7 HD71 sing N N 17 A4C CD7 HD72 sing N N 18 A4C CD7 HD73 sing N N 19 A4C C4 C3 doub Y N 20 A4C C4 C12 sing Y N 21 A4C C3 C2 sing Y N 22 A4C C3 H3 sing N N 23 A4C C2 C1 doub Y N 24 A4C C2 H2 sing N N 25 A4C C12 C11 sing Y N 26 A4C C12 N10 doub Y N 27 A4C C11 C1 sing Y N 28 A4C C11 C9 doub Y N 29 A4C C1 H1 sing N N 30 A4C N10 C14 sing Y N 31 A4C C14 C5 doub Y N 32 A4C C14 C13 sing Y N 33 A4C C5 C6 sing Y N 34 A4C C5 H5 sing N N 35 A4C C6 C7 doub Y N 36 A4C C6 H6 sing N N 37 A4C C7 C8 sing Y N 38 A4C C7 H7 sing N N 39 A4C C13 C8 doub Y N 40 A4C C13 C9 sing Y N 41 A4C C8 H8 sing N N 42 A4C C9 N9 sing N N 43 A4C N9 CX1 sing N N 44 A4C N9 HN9 sing N N 45 A4C CX1 CX2 sing N N 46 A4C CX1 HX11 sing N N 47 A4C CX1 HX12 sing N N 48 A4C CX2 CX3 sing N N 49 A4C CX2 HX21 sing N N 50 A4C CX2 HX22 sing N N 51 A4C CX3 CX6 sing N N 52 A4C CX3 HX31 sing N N 53 A4C CX3 HX32 sing N N 54 A4C OD2 CD4 doub N N 55 A4C CD4 ND3 sing N N 56 A4C CD4 C25 sing N N 57 A4C ND3 CD5 sing N N 58 A4C ND3 HND3 sing N N 59 A4C CD5 CD6 sing N N 60 A4C CD5 HD51 sing N N 61 A4C CD5 HD52 sing N N 62 A4C CD6 ND4 sing N N 63 A4C CD6 HD61 sing N N 64 A4C CD6 HD62 sing N N 65 A4C ND4 CD0 sing N N 66 A4C ND4 CD9 sing N N 67 A4C CD0 HD01 sing N N 68 A4C CD0 HD02 sing N N 69 A4C CD0 HD03 sing N N 70 A4C CD9 HD91 sing N N 71 A4C CD9 HD92 sing N N 72 A4C CD9 HD93 sing N N 73 A4C C25 C26 sing Y N 74 A4C C25 C27 doub Y N 75 A4C C26 C15 doub Y N 76 A4C C26 H26 sing N N 77 A4C C15 C17 sing Y N 78 A4C C15 H15 sing N N 79 A4C C27 C16 sing Y N 80 A4C C27 N12 sing Y N 81 A4C C16 C17 doub Y N 82 A4C C16 C24 sing Y N 83 A4C C17 H17 sing N N 84 A4C N12 C18 doub Y N 85 A4C C18 C19 sing Y N 86 A4C C18 C22 sing Y N 87 A4C C19 C20 doub Y N 88 A4C C19 H19 sing N N 89 A4C C20 C21 sing Y N 90 A4C C20 H20 sing N N 91 A4C C21 C23 doub Y N 92 A4C C21 H21 sing N N 93 A4C C22 C23 sing Y N 94 A4C C22 C24 doub Y N 95 A4C C23 H23 sing N N 96 A4C C24 N11 sing N N 97 A4C N11 CX4 sing N N 98 A4C N11 HN11 sing N N 99 A4C CX4 CX5 sing N N 100 A4C CX4 HX41 sing N N 101 A4C CX4 HX42 sing N N 102 A4C CX5 CX6 sing N N 103 A4C CX5 HX51 sing N N 104 A4C CX5 HX52 sing N N 105 A4C CX6 HX61 sing N N 106 A4C CX6 HX62 sing N N 107 DA OP3 P sing N N 108 DA OP3 HOP3 sing N N 109 DA P OP1 doub N N 110 DA P OP2 sing N N 111 DA P "O5'" sing N N 112 DA OP2 HOP2 sing N N 113 DA "O5'" "C5'" sing N N 114 DA "C5'" "C4'" sing N N 115 DA "C5'" "H5'" sing N N 116 DA "C5'" "H5''" sing N N 117 DA "C4'" "O4'" sing N N 118 DA "C4'" "C3'" sing N N 119 DA "C4'" "H4'" sing N N 120 DA "O4'" "C1'" sing N N 121 DA "C3'" "O3'" sing N N 122 DA "C3'" "C2'" sing N N 123 DA "C3'" "H3'" sing N N 124 DA "O3'" "HO3'" sing N N 125 DA "C2'" "C1'" sing N N 126 DA "C2'" "H2'" sing N N 127 DA "C2'" "H2''" sing N N 128 DA "C1'" N9 sing N N 129 DA "C1'" "H1'" sing N N 130 DA N9 C8 sing Y N 131 DA N9 C4 sing Y N 132 DA C8 N7 doub Y N 133 DA C8 H8 sing N N 134 DA N7 C5 sing Y N 135 DA C5 C6 sing Y N 136 DA C5 C4 doub Y N 137 DA C6 N6 sing N N 138 DA C6 N1 doub Y N 139 DA N6 H61 sing N N 140 DA N6 H62 sing N N 141 DA N1 C2 sing Y N 142 DA C2 N3 doub Y N 143 DA C2 H2 sing N N 144 DA N3 C4 sing Y N 145 DC OP3 P sing N N 146 DC OP3 HOP3 sing N N 147 DC P OP1 doub N N 148 DC P OP2 sing N N 149 DC P "O5'" sing N N 150 DC OP2 HOP2 sing N N 151 DC "O5'" "C5'" sing N N 152 DC "C5'" "C4'" sing N N 153 DC "C5'" "H5'" sing N N 154 DC "C5'" "H5''" sing N N 155 DC "C4'" "O4'" sing N N 156 DC "C4'" "C3'" sing N N 157 DC "C4'" "H4'" sing N N 158 DC "O4'" "C1'" sing N N 159 DC "C3'" "O3'" sing N N 160 DC "C3'" "C2'" sing N N 161 DC "C3'" "H3'" sing N N 162 DC "O3'" "HO3'" sing N N 163 DC "C2'" "C1'" sing N N 164 DC "C2'" "H2'" sing N N 165 DC "C2'" "H2''" sing N N 166 DC "C1'" N1 sing N N 167 DC "C1'" "H1'" sing N N 168 DC N1 C2 sing N N 169 DC N1 C6 sing N N 170 DC C2 O2 doub N N 171 DC C2 N3 sing N N 172 DC N3 C4 doub N N 173 DC C4 N4 sing N N 174 DC C4 C5 sing N N 175 DC N4 H41 sing N N 176 DC N4 H42 sing N N 177 DC C5 C6 doub N N 178 DC C5 H5 sing N N 179 DC C6 H6 sing N N 180 DG OP3 P sing N N 181 DG OP3 HOP3 sing N N 182 DG P OP1 doub N N 183 DG P OP2 sing N N 184 DG P "O5'" sing N N 185 DG OP2 HOP2 sing N N 186 DG "O5'" "C5'" sing N N 187 DG "C5'" "C4'" sing N N 188 DG "C5'" "H5'" sing N N 189 DG "C5'" "H5''" sing N N 190 DG "C4'" "O4'" sing N N 191 DG "C4'" "C3'" sing N N 192 DG "C4'" "H4'" sing N N 193 DG "O4'" "C1'" sing N N 194 DG "C3'" "O3'" sing N N 195 DG "C3'" "C2'" sing N N 196 DG "C3'" "H3'" sing N N 197 DG "O3'" "HO3'" sing N N 198 DG "C2'" "C1'" sing N N 199 DG "C2'" "H2'" sing N N 200 DG "C2'" "H2''" sing N N 201 DG "C1'" N9 sing N N 202 DG "C1'" "H1'" sing N N 203 DG N9 C8 sing Y N 204 DG N9 C4 sing Y N 205 DG C8 N7 doub Y N 206 DG C8 H8 sing N N 207 DG N7 C5 sing Y N 208 DG C5 C6 sing N N 209 DG C5 C4 doub Y N 210 DG C6 O6 doub N N 211 DG C6 N1 sing N N 212 DG N1 C2 sing N N 213 DG N1 H1 sing N N 214 DG C2 N2 sing N N 215 DG C2 N3 doub N N 216 DG N2 H21 sing N N 217 DG N2 H22 sing N N 218 DG N3 C4 sing N N 219 DT OP3 P sing N N 220 DT OP3 HOP3 sing N N 221 DT P OP1 doub N N 222 DT P OP2 sing N N 223 DT P "O5'" sing N N 224 DT OP2 HOP2 sing N N 225 DT "O5'" "C5'" sing N N 226 DT "C5'" "C4'" sing N N 227 DT "C5'" "H5'" sing N N 228 DT "C5'" "H5''" sing N N 229 DT "C4'" "O4'" sing N N 230 DT "C4'" "C3'" sing N N 231 DT "C4'" "H4'" sing N N 232 DT "O4'" "C1'" sing N N 233 DT "C3'" "O3'" sing N N 234 DT "C3'" "C2'" sing N N 235 DT "C3'" "H3'" sing N N 236 DT "O3'" "HO3'" sing N N 237 DT "C2'" "C1'" sing N N 238 DT "C2'" "H2'" sing N N 239 DT "C2'" "H2''" sing N N 240 DT "C1'" N1 sing N N 241 DT "C1'" "H1'" sing N N 242 DT N1 C2 sing N N 243 DT N1 C6 sing N N 244 DT C2 O2 doub N N 245 DT C2 N3 sing N N 246 DT N3 C4 sing N N 247 DT N3 H3 sing N N 248 DT C4 O4 doub N N 249 DT C4 C5 sing N N 250 DT C5 C7 sing N N 251 DT C5 C6 doub N N 252 DT C7 H71 sing N N 253 DT C7 H72 sing N N 254 DT C7 H73 sing N N 255 DT C6 H6 sing N N 256 HOH O H1 sing N N 257 HOH O H2 sing N N 258 # _ndb_struct_conf_na.entry_id 2GB9 _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 1 1_555 B DG 6 1_555 0.377 -0.134 0.140 1.132 -8.296 -0.572 1 A_DC1:DG6_B A 1 ? B 6 ? 19 1 1 A DG 2 1_555 B DC 5 1_555 -0.305 -0.218 0.102 1.953 -11.268 0.248 2 A_DG2:DC5_B A 2 ? B 5 ? 19 1 1 A DT 3 1_555 B DA 4 1_555 0.063 -0.133 -0.016 5.843 -9.357 3.210 3 A_DT3:DA4_B A 3 ? B 4 ? 20 1 1 A DA 4 1_555 B DT 3 1_555 0.036 -0.143 0.122 -0.330 -8.202 2.199 4 A_DA4:DT3_B A 4 ? B 3 ? 20 1 1 A DC 5 1_555 B DG 2 1_555 0.193 -0.129 -0.197 8.041 -1.115 -0.823 5 A_DC5:DG2_B A 5 ? B 2 ? 19 1 1 A DG 6 1_555 B DC 1 1_555 -0.249 -0.065 0.190 6.143 -9.093 1.298 6 A_DG6:DC1_B A 6 ? B 1 ? 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 6 1_555 A DG 2 1_555 B DC 5 1_555 -0.166 0.313 6.738 5.244 10.987 18.818 -7.716 4.494 5.789 29.887 -14.266 22.382 1 AA_DC1DG2:DC5DG6_BB A 1 ? B 6 ? A 2 ? B 5 ? 1 A DG 2 1_555 B DC 5 1_555 A DT 3 1_555 B DA 4 1_555 0.414 -0.356 3.163 0.691 2.027 31.856 -1.002 -0.632 3.143 3.688 -1.256 31.926 2 AA_DG2DT3:DA4DC5_BB A 2 ? B 5 ? A 3 ? B 4 ? 1 A DT 3 1_555 B DA 4 1_555 A DA 4 1_555 B DT 3 1_555 0.156 -0.187 3.386 0.782 4.975 36.630 -0.987 -0.137 3.335 7.869 -1.236 36.963 3 AA_DT3DA4:DT3DA4_BB A 3 ? B 4 ? A 4 ? B 3 ? 1 A DA 4 1_555 B DT 3 1_555 A DC 5 1_555 B DG 2 1_555 0.279 -0.240 3.073 3.868 4.421 24.332 -1.788 0.436 2.991 10.297 -9.010 25.020 4 AA_DA4DC5:DG2DT3_BB A 4 ? B 3 ? A 5 ? B 2 ? 1 A DC 5 1_555 B DG 2 1_555 A DG 6 1_555 B DC 1 1_555 -0.194 0.747 6.820 2.245 4.898 21.938 -1.862 2.223 6.770 12.626 -5.789 22.582 5 AA_DC5DG6:DC1DG2_BB A 5 ? B 2 ? A 6 ? B 1 ? # _atom_sites.entry_id 2GB9 _atom_sites.fract_transf_matrix[1][1] 0.026874 _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] 0.026874 _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] 0.018699 _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 SR # loop_