data_4OCD # _entry.id 4OCD # _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 4OCD pdb_00004ocd 10.2210/pdb4ocd/pdb NDB NA2876 ? ? RCSB RCSB084314 ? ? WWPDB D_1000084314 ? ? # 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 2014-06-11 2 'Structure model' 1 1 2024-02-28 # _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' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 '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 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 4 2 '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 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 2 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 2 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4OCD _pdbx_database_status.recvd_initial_deposition_date 2014-01-08 _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.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Acosta-Reyes, F.J.' 1 'Dardonville, C.' 2 'de Koning, H.P.' 3 'Natto, M.' 4 'Subirana, J.A.' 5 'Campos, J.L.' 6 # _citation.id primary _citation.title 'In and out of the minor groove: interaction of an AT-rich DNA with the drug CD27' _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume D70 _citation.page_first 1614 _citation.page_last 1621 _citation.year 2014 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24914972 _citation.pdbx_database_id_DOI 10.1107/S139900471400697X # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Acosta-Reyes, F.J.' 1 ? primary 'Dardonville, C.' 2 ? primary 'de Koning, H.P.' 3 ? primary 'Natto, M.' 4 ? primary 'Subirana, J.A.' 5 ? primary 'Campos, J.L.' 6 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'd(AAAATTTT)' 2424.641 3 ? ? ? ? 2 non-polymer syn 'N1-(4,5-dihydro-1H-imidazol-2-yl)-N4-(4-((4,5-dihydro-1H-imidazol-2-yl)amino)phenyl)benzene-1,4-diamine' 335.406 3 ? ? ? ? 3 water nat water 18.015 64 ? ? ? ? # _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 '(DA)(DA)(DA)(DA)(DT)(DT)(DT)(DT)' _entity_poly.pdbx_seq_one_letter_code_can AAAATTTT _entity_poly.pdbx_strand_id A,B,C _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'N1-(4,5-dihydro-1H-imidazol-2-yl)-N4-(4-((4,5-dihydro-1H-imidazol-2-yl)amino)phenyl)benzene-1,4-diamine' MWB 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DA n 1 2 DA n 1 3 DA n 1 4 DA n 1 5 DT n 1 6 DT n 1 7 DT n 1 8 DT n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 MWB non-polymer . 'N1-(4,5-dihydro-1H-imidazol-2-yl)-N4-(4-((4,5-dihydro-1H-imidazol-2-yl)amino)phenyl)benzene-1,4-diamine' CD27 'C18 H21 N7' 335.406 # 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 DA 1 1 1 DA DA A . n A 1 2 DA 2 2 2 DA DA A . n A 1 3 DA 3 3 3 DA DA A . n A 1 4 DA 4 4 4 DA DA A . n A 1 5 DT 5 5 5 DT DT A . n A 1 6 DT 6 6 6 DT DT A . n A 1 7 DT 7 7 7 DT DT A . n A 1 8 DT 8 8 8 DT DT A . n B 1 1 DA 1 1 1 DA DA B . n B 1 2 DA 2 2 2 DA DA B . n B 1 3 DA 3 3 3 DA DA B . n B 1 4 DA 4 4 4 DA DA B . n B 1 5 DT 5 5 5 DT DT B . n B 1 6 DT 6 6 6 DT DT B . n B 1 7 DT 7 7 7 DT DT B . n B 1 8 DT 8 8 8 DT DT B . n C 1 1 DA 1 1 1 DA DA C . n C 1 2 DA 2 2 2 DA DA C . n C 1 3 DA 3 3 3 DA DA C . n C 1 4 DA 4 4 4 DA DA C . n C 1 5 DT 5 5 5 DT DT C . n C 1 6 DT 6 6 6 DT DT C . n C 1 7 DT 7 7 7 DT DT C . n C 1 8 DT 8 8 8 DT DT C . 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 D 2 MWB 1 101 1 MWB MWB A . E 2 MWB 1 101 1 MWB MWB B . F 2 MWB 1 101 1 MWB MWB C . G 3 HOH 1 201 1 HOH HOH A . G 3 HOH 2 202 6 HOH HOH A . G 3 HOH 3 203 8 HOH HOH A . G 3 HOH 4 204 12 HOH HOH A . G 3 HOH 5 205 13 HOH HOH A . G 3 HOH 6 206 20 HOH HOH A . G 3 HOH 7 207 24 HOH HOH A . G 3 HOH 8 208 25 HOH HOH A . G 3 HOH 9 209 27 HOH HOH A . G 3 HOH 10 210 31 HOH HOH A . G 3 HOH 11 211 33 HOH HOH A . G 3 HOH 12 212 34 HOH HOH A . G 3 HOH 13 213 36 HOH HOH A . G 3 HOH 14 214 38 HOH HOH A . G 3 HOH 15 215 41 HOH HOH A . G 3 HOH 16 216 48 HOH HOH A . G 3 HOH 17 217 52 HOH HOH A . G 3 HOH 18 218 60 HOH HOH A . G 3 HOH 19 219 61 HOH HOH A . G 3 HOH 20 220 63 HOH HOH A . G 3 HOH 21 221 64 HOH HOH A . G 3 HOH 22 222 65 HOH HOH A . G 3 HOH 23 223 67 HOH HOH A . G 3 HOH 24 224 70 HOH HOH A . G 3 HOH 25 225 71 HOH HOH A . G 3 HOH 26 226 72 HOH HOH A . G 3 HOH 27 227 73 HOH HOH A . G 3 HOH 28 228 74 HOH HOH A . G 3 HOH 29 229 75 HOH HOH A . G 3 HOH 30 230 82 HOH HOH A . G 3 HOH 31 231 83 HOH HOH A . G 3 HOH 32 232 86 HOH HOH A . G 3 HOH 33 233 89 HOH HOH A . G 3 HOH 34 234 91 HOH HOH A . H 3 HOH 1 201 2 HOH HOH B . H 3 HOH 2 202 7 HOH HOH B . H 3 HOH 3 203 10 HOH HOH B . H 3 HOH 4 204 14 HOH HOH B . H 3 HOH 5 205 15 HOH HOH B . H 3 HOH 6 206 16 HOH HOH B . H 3 HOH 7 207 18 HOH HOH B . H 3 HOH 8 208 23 HOH HOH B . H 3 HOH 9 209 30 HOH HOH B . H 3 HOH 10 210 37 HOH HOH B . H 3 HOH 11 211 40 HOH HOH B . H 3 HOH 12 212 55 HOH HOH B . H 3 HOH 13 213 59 HOH HOH B . H 3 HOH 14 214 62 HOH HOH B . H 3 HOH 15 215 69 HOH HOH B . H 3 HOH 16 216 80 HOH HOH B . H 3 HOH 17 217 84 HOH HOH B . H 3 HOH 18 218 87 HOH HOH B . H 3 HOH 19 219 90 HOH HOH B . H 3 HOH 20 220 93 HOH HOH B . I 3 HOH 1 201 3 HOH HOH C . I 3 HOH 2 202 17 HOH HOH C . I 3 HOH 3 203 22 HOH HOH C . I 3 HOH 4 204 29 HOH HOH C . I 3 HOH 5 205 50 HOH HOH C . I 3 HOH 6 206 54 HOH HOH C . I 3 HOH 7 207 66 HOH HOH C . I 3 HOH 8 208 68 HOH HOH C . I 3 HOH 9 209 85 HOH HOH C . I 3 HOH 10 210 92 HOH HOH C . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal PHASER phasing . ? 1 REFMAC refinement 5.8.0049 ? 2 XDS 'data reduction' . ? 3 SCALA 'data scaling' . ? 4 # _cell.entry_id 4OCD _cell.length_a 78.013 _cell.length_b 78.013 _cell.length_c 91.552 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 36 _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 4OCD _symmetry.space_group_name_H-M 'P 61 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4OCD _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 288.15 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details ;0.25 mM DNA duplex, 0.75 mM CD27, 40 mM sodium cacodylate buffer pH 6.5, 8 mM MnCl2 , 0.5 mM spermine and 5% MPD equilibrated against a 30% MPD reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 288.15 K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector PIXEL _diffrn_detector.type 'DECTRIS PILATUS 6M' _diffrn_detector.pdbx_collection_date 2013-07-19 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Channel-cut Si(111), KB focusing mirrors' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97949 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ALBA BEAMLINE XALOC' _diffrn_source.pdbx_synchrotron_site ALBA _diffrn_source.pdbx_synchrotron_beamline XALOC _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.97949 # _reflns.entry_id 4OCD _reflns.observed_criterion_sigma_I 2 _reflns.observed_criterion_sigma_F 2 _reflns.d_resolution_low 39 _reflns.d_resolution_high 2.1 _reflns.number_obs 10091 _reflns.number_all ? _reflns.percent_possible_obs 99.8 _reflns.pdbx_Rmerge_I_obs 0.036 _reflns.pdbx_Rsym_value 0.036 _reflns.pdbx_netI_over_sigmaI 30.2 _reflns.B_iso_Wilson_estimate 59.64 _reflns.pdbx_redundancy 11.4 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_unique_obs _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 2.10 2.21 99.84 0.58 ? 3.00 6.85 ? 1433 ? ? ? ? 1 1 2.21 2.35 100.00 0.49 ? 4.66 10.38 ? 1367 ? ? ? ? 2 1 2.35 2.51 99.96 0.27 ? 9.12 13.05 ? 1290 ? ? ? ? 3 1 2.51 2.71 99.90 0.15 ? 14.48 12.79 ? 1194 ? ? ? ? 4 1 2.71 2.97 99.98 0.07 ? 27.70 12.87 ? 1115 ? ? ? ? 5 1 2.97 3.32 99.42 0.03 ? 42.17 12.56 ? 1006 ? ? ? ? 6 1 3.32 3.83 99.90 0.03 ? 64.47 12.46 ? 907 ? ? ? ? 7 1 3.83 4.70 99.73 0.03 ? 74.68 12.00 ? 778 ? ? ? ? 8 1 4.70 6.64 99.34 0.03 ? 75.19 11.83 ? 625 ? ? ? ? 9 1 6.64 39.00 98.22 0.02 ? 74.71 10.1 ? 376 ? ? ? ? 10 1 # _refine.entry_id 4OCD _refine.ls_number_reflns_obs 9432 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F . _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 39 _refine.ls_d_res_high 2.10 _refine.ls_percent_reflns_obs 97.91 _refine.ls_R_factor_obs 0.23682 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.23614 _refine.ls_R_factor_R_free 0.25103 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.8 _refine.ls_number_reflns_R_free 480 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.956 _refine.correlation_coeff_Fo_to_Fc_free 0.968 _refine.B_iso_mean 60.320 _refine.aniso_B[1][1] -3.21 _refine.aniso_B[2][2] -3.21 _refine.aniso_B[3][3] 10.42 _refine.aniso_B[1][2] -1.61 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.152 _refine.pdbx_overall_ESU_R_Free 0.139 _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_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 483 _refine_hist.pdbx_number_atoms_ligand 75 _refine_hist.number_atoms_solvent 64 _refine_hist.number_atoms_total 622 _refine_hist.d_res_high 2.10 _refine_hist.d_res_low 39 # 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_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 0.024 0.011 ? 635 ? 'X-RAY DIFFRACTION' r_bond_other_d 0.008 0.018 ? 348 ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1.653 1.281 ? 939 ? 'X-RAY DIFFRACTION' r_angle_other_deg 7.222 3.000 ? 813 ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_4_deg ? ? ? ? ? 'X-RAY DIFFRACTION' r_chiral_restr 0.069 0.200 ? 72 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.008 0.020 ? 594 ? 'X-RAY DIFFRACTION' r_gen_planes_other 0.006 0.020 ? 126 ? 'X-RAY DIFFRACTION' r_nbd_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbd_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbtor_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_nbtor_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_xyhbond_nbd_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_xyhbond_nbd_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_metal_ion_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_metal_ion_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_vdw_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_vdw_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_hbond_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_hbond_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_metal_ion_refined ? ? ? ? ? 'X-RAY DIFFRACTION' r_symmetry_metal_ion_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcbond_it 9.295 5.949 ? 4 ? 'X-RAY DIFFRACTION' r_mcbond_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcangle_it ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcangle_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_scbond_it 7.309 6.208 ? 631 ? 'X-RAY DIFFRACTION' r_scbond_other 7.303 6.211 ? 632 ? 'X-RAY DIFFRACTION' r_scangle_it ? ? ? ? ? 'X-RAY DIFFRACTION' r_scangle_other 10.895 9.310 ? 940 ? 'X-RAY DIFFRACTION' r_long_range_B_refined 13.348 59.013 ? 2600 ? 'X-RAY DIFFRACTION' r_long_range_B_other 13.424 58.974 ? 2548 ? 'X-RAY DIFFRACTION' r_rigid_bond_restr ? ? ? ? ? 'X-RAY DIFFRACTION' r_sphericity_free ? ? ? ? ? 'X-RAY DIFFRACTION' r_sphericity_bonded ? ? ? ? ? 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.100 _refine_ls_shell.d_res_low 2.154 _refine_ls_shell.number_reflns_R_work 622 _refine_ls_shell.R_factor_R_work 0.437 _refine_ls_shell.percent_reflns_obs 89.82 _refine_ls_shell.R_factor_R_free 0.455 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 31 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 4OCD _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 4OCD _struct.title 'In and Out the minor groove: Interaction of an AT rich-DNA with the CD27 drug' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4OCD _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA minor groove binding drugs, all-AT DNA, dicationic drug, imidazoline drug, 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 1 ? D N N 2 ? E N N 2 ? F N N 2 ? G N N 3 ? H N N 3 ? I N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4OCD _struct_ref.pdbx_db_accession 4OCD _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code AAAATTTT _struct_ref.pdbx_db_isoform ? # 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 4OCD A 1 ? 8 ? 4OCD 1 ? 8 ? 1 8 2 1 4OCD B 1 ? 8 ? 4OCD 1 ? 8 ? 1 8 3 1 4OCD C 1 ? 8 ? 4OCD 1 ? 8 ? 1 8 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA dimeric 2 2 author_and_software_defined_assembly PISA dimeric 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 680 ? 1 MORE -6 ? 1 'SSA (A^2)' 3160 ? 2 'ABSA (A^2)' 680 ? 2 MORE -7 ? 2 'SSA (A^2)' 3120 ? # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1,2 A,D,G 2 1 B,C,E,F,H,I # 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' 12_555 x,x-y,-z+1/6 0.5000000000 0.8660254038 0.0000000000 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 15.2586666667 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? B DA 1 N1 ? ? ? 1_555 C DT 8 N3 ? ? B DA 1 C DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? B DA 1 N6 ? ? ? 1_555 C DT 8 O4 ? ? B DA 1 C DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? B DA 2 N1 ? ? ? 1_555 C DT 7 N3 ? ? B DA 2 C DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? B DA 2 N6 ? ? ? 1_555 C DT 7 O4 ? ? B DA 2 C DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? B DA 3 N1 ? ? ? 1_555 C DT 6 N3 ? ? B DA 3 C DT 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? B DA 3 N6 ? ? ? 1_555 C DT 6 O4 ? ? B DA 3 C DT 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? B DA 4 N1 ? ? ? 1_555 C DT 5 N3 ? ? B DA 4 C DT 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? B DA 4 N6 ? ? ? 1_555 C DT 5 O4 ? ? B DA 4 C DT 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? B DT 5 N3 ? ? ? 1_555 C DA 4 N1 ? ? B DT 5 C DA 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? B DT 5 O4 ? ? ? 1_555 C DA 4 N6 ? ? B DT 5 C DA 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? B DT 6 N3 ? ? ? 1_555 C DA 3 N1 ? ? B DT 6 C DA 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? B DT 6 O4 ? ? ? 1_555 C DA 3 N6 ? ? B DT 6 C DA 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? B DT 7 N3 ? ? ? 1_555 C DA 2 N1 ? ? B DT 7 C DA 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? B DT 7 O4 ? ? ? 1_555 C DA 2 N6 ? ? B DT 7 C DA 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? B DT 8 N3 ? ? ? 1_555 C DA 1 N1 ? ? B DT 8 C DA 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? B DT 8 O4 ? ? ? 1_555 C DA 1 N6 ? ? B DT 8 C DA 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 1 N1 ? ? ? 1_555 A DT 8 N3 ? ? A DA 1 A DT 8 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DA 1 N6 ? ? ? 1_555 A DT 8 O4 ? ? A DA 1 A DT 8 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DA 2 N1 ? ? ? 1_555 A DT 7 N3 ? ? A DA 2 A DT 7 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DA 2 N6 ? ? ? 1_555 A DT 7 O4 ? ? A DA 2 A DT 7 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DA 3 N1 ? ? ? 1_555 A DT 6 N3 ? ? A DA 3 A DT 6 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DA 3 N6 ? ? ? 1_555 A DT 6 O4 ? ? A DA 3 A DT 6 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DA 4 N1 ? ? ? 1_555 A DT 5 N3 ? ? A DA 4 A DT 5 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DA 4 N6 ? ? ? 1_555 A DT 5 O4 ? ? A DA 4 A DT 5 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DT 5 N3 ? ? ? 1_555 A DA 4 N1 ? ? A DT 5 A DA 4 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DT 5 O4 ? ? ? 1_555 A DA 4 N6 ? ? A DT 5 A DA 4 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DT 6 N3 ? ? ? 1_555 A DA 3 N1 ? ? A DT 6 A DA 3 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DT 6 O4 ? ? ? 1_555 A DA 3 N6 ? ? A DT 6 A DA 3 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DT 7 N3 ? ? ? 1_555 A DA 2 N1 ? ? A DT 7 A DA 2 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DT 7 O4 ? ? ? 1_555 A DA 2 N6 ? ? A DT 7 A DA 2 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DT 8 N3 ? ? ? 1_555 A DA 1 N1 ? ? A DT 8 A DA 1 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DT 8 O4 ? ? ? 1_555 A DA 1 N6 ? ? A DT 8 A DA 1 12_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 MWB 101 ? 16 'BINDING SITE FOR RESIDUE MWB A 101' AC2 Software B MWB 101 ? 15 'BINDING SITE FOR RESIDUE MWB B 101' AC3 Software C MWB 101 ? 11 'BINDING SITE FOR RESIDUE MWB C 101' # 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 16 DA A 1 ? DA A 1 . ? 12_555 ? 2 AC1 16 DA A 2 ? DA A 2 . ? 12_555 ? 3 AC1 16 DA A 3 ? DA A 3 . ? 12_555 ? 4 AC1 16 DA A 4 ? DA A 4 . ? 12_555 ? 5 AC1 16 DT A 5 ? DT A 5 . ? 1_555 ? 6 AC1 16 DT A 5 ? DT A 5 . ? 12_555 ? 7 AC1 16 DT A 6 ? DT A 6 . ? 1_555 ? 8 AC1 16 DT A 7 ? DT A 7 . ? 1_555 ? 9 AC1 16 DT A 8 ? DT A 8 . ? 1_555 ? 10 AC1 16 HOH G . ? HOH A 202 . ? 1_555 ? 11 AC1 16 HOH G . ? HOH A 211 . ? 1_555 ? 12 AC1 16 HOH G . ? HOH A 213 . ? 1_555 ? 13 AC1 16 DA B 2 ? DA B 2 . ? 7_555 ? 14 AC1 16 DA B 3 ? DA B 3 . ? 7_555 ? 15 AC1 16 MWB E . ? MWB B 101 . ? 1_555 ? 16 AC1 16 DT C 8 ? DT C 8 . ? 1_555 ? 17 AC2 15 DT A 8 ? DT A 8 . ? 1_555 ? 18 AC2 15 MWB D . ? MWB A 101 . ? 1_555 ? 19 AC2 15 DA B 1 ? DA B 1 . ? 1_555 ? 20 AC2 15 DA B 2 ? DA B 2 . ? 1_555 ? 21 AC2 15 DA B 3 ? DA B 3 . ? 1_555 ? 22 AC2 15 DA B 3 ? DA B 3 . ? 7_555 ? 23 AC2 15 DA B 4 ? DA B 4 . ? 1_555 ? 24 AC2 15 DT B 5 ? DT B 5 . ? 1_555 ? 25 AC2 15 HOH H . ? HOH B 202 . ? 1_555 ? 26 AC2 15 HOH H . ? HOH B 208 . ? 1_555 ? 27 AC2 15 DT C 5 ? DT C 5 . ? 1_555 ? 28 AC2 15 DT C 6 ? DT C 6 . ? 1_555 ? 29 AC2 15 DT C 7 ? DT C 7 . ? 1_555 ? 30 AC2 15 DT C 8 ? DT C 8 . ? 1_555 ? 31 AC2 15 MWB F . ? MWB C 101 . ? 1_555 ? 32 AC3 11 DT B 5 ? DT B 5 . ? 1_555 ? 33 AC3 11 DT B 6 ? DT B 6 . ? 1_555 ? 34 AC3 11 DT B 7 ? DT B 7 . ? 1_555 ? 35 AC3 11 DT B 8 ? DT B 8 . ? 12_545 ? 36 AC3 11 DT B 8 ? DT B 8 . ? 1_555 ? 37 AC3 11 MWB E . ? MWB B 101 . ? 1_555 ? 38 AC3 11 DA C 1 ? DA C 1 . ? 1_555 ? 39 AC3 11 DA C 2 ? DA C 2 . ? 1_555 ? 40 AC3 11 DA C 3 ? DA C 3 . ? 1_555 ? 41 AC3 11 DA C 4 ? DA C 4 . ? 1_555 ? 42 AC3 11 DT C 5 ? DT C 5 . ? 1_555 ? # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 220 ? G HOH . 2 1 B HOH 214 ? H HOH . # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DT OP3 O N N 37 DT P P N N 38 DT OP1 O N N 39 DT OP2 O N N 40 DT "O5'" O N N 41 DT "C5'" C N N 42 DT "C4'" C N R 43 DT "O4'" O N N 44 DT "C3'" C N S 45 DT "O3'" O N N 46 DT "C2'" C N N 47 DT "C1'" C N R 48 DT N1 N N N 49 DT C2 C N N 50 DT O2 O N N 51 DT N3 N N N 52 DT C4 C N N 53 DT O4 O N N 54 DT C5 C N N 55 DT C7 C N N 56 DT C6 C N N 57 DT HOP3 H N N 58 DT HOP2 H N N 59 DT "H5'" H N N 60 DT "H5''" H N N 61 DT "H4'" H N N 62 DT "H3'" H N N 63 DT "HO3'" H N N 64 DT "H2'" H N N 65 DT "H2''" H N N 66 DT "H1'" H N N 67 DT H3 H N N 68 DT H71 H N N 69 DT H72 H N N 70 DT H73 H N N 71 DT H6 H N N 72 HOH O O N N 73 HOH H1 H N N 74 HOH H2 H N N 75 MWB C1 C Y N 76 MWB C2 C Y N 77 MWB C3 C Y N 78 MWB C4 C Y N 79 MWB C5 C Y N 80 MWB C6 C Y N 81 MWB C7 C Y N 82 MWB C8 C Y N 83 MWB C9 C Y N 84 MWB C10 C Y N 85 MWB C11 C Y N 86 MWB C12 C Y N 87 MWB N1 N N N 88 MWB C13 C N N 89 MWB N2 N N N 90 MWB N3 N N N 91 MWB C14 C N N 92 MWB N4 N N N 93 MWB N5 N N N 94 MWB N6 N N N 95 MWB N7 N N N 96 MWB C15 C N N 97 MWB C16 C N N 98 MWB C17 C N N 99 MWB C18 C N N 100 MWB H1 H N N 101 MWB H2 H N N 102 MWB H3 H N N 103 MWB H4 H N N 104 MWB H5 H N N 105 MWB H6 H N N 106 MWB H7 H N N 107 MWB H8 H N N 108 MWB H9 H N N 109 MWB H10 H N N 110 MWB H15 H N N 111 MWB H17 H N N 112 MWB H18 H N N 113 MWB H19 H N N 114 MWB H20 H N N 115 MWB H21 H N N 116 MWB H22 H N N 117 MWB H23 H N N 118 MWB H24 H N N 119 MWB H11 H N N 120 MWB H12 H N N 121 # 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 DT OP3 P sing N N 39 DT OP3 HOP3 sing N N 40 DT P OP1 doub N N 41 DT P OP2 sing N N 42 DT P "O5'" sing N N 43 DT OP2 HOP2 sing N N 44 DT "O5'" "C5'" sing N N 45 DT "C5'" "C4'" sing N N 46 DT "C5'" "H5'" sing N N 47 DT "C5'" "H5''" sing N N 48 DT "C4'" "O4'" sing N N 49 DT "C4'" "C3'" sing N N 50 DT "C4'" "H4'" sing N N 51 DT "O4'" "C1'" sing N N 52 DT "C3'" "O3'" sing N N 53 DT "C3'" "C2'" sing N N 54 DT "C3'" "H3'" sing N N 55 DT "O3'" "HO3'" sing N N 56 DT "C2'" "C1'" sing N N 57 DT "C2'" "H2'" sing N N 58 DT "C2'" "H2''" sing N N 59 DT "C1'" N1 sing N N 60 DT "C1'" "H1'" sing N N 61 DT N1 C2 sing N N 62 DT N1 C6 sing N N 63 DT C2 O2 doub N N 64 DT C2 N3 sing N N 65 DT N3 C4 sing N N 66 DT N3 H3 sing N N 67 DT C4 O4 doub N N 68 DT C4 C5 sing N N 69 DT C5 C7 sing N N 70 DT C5 C6 doub N N 71 DT C7 H71 sing N N 72 DT C7 H72 sing N N 73 DT C7 H73 sing N N 74 DT C6 H6 sing N N 75 HOH O H1 sing N N 76 HOH O H2 sing N N 77 MWB C17 C18 sing N N 78 MWB C17 N4 sing N N 79 MWB C16 C15 sing N N 80 MWB C16 N3 sing N N 81 MWB C18 N5 sing N N 82 MWB C15 N2 sing N N 83 MWB N4 C14 doub N N 84 MWB N3 C13 doub N N 85 MWB N5 C14 sing N N 86 MWB C14 N6 sing N N 87 MWB N2 C13 sing N N 88 MWB C3 C6 doub Y N 89 MWB C3 C1 sing Y N 90 MWB C13 N7 sing N N 91 MWB C6 C2 sing Y N 92 MWB N6 C1 sing N N 93 MWB C10 C7 doub Y N 94 MWB C10 C11 sing Y N 95 MWB C1 C4 doub Y N 96 MWB C7 C9 sing Y N 97 MWB N7 C11 sing N N 98 MWB C11 C8 doub Y N 99 MWB C2 N1 sing N N 100 MWB C2 C5 doub Y N 101 MWB C9 N1 sing N N 102 MWB C9 C12 doub Y N 103 MWB C4 C5 sing Y N 104 MWB C8 C12 sing Y N 105 MWB C3 H1 sing N N 106 MWB C4 H2 sing N N 107 MWB C5 H3 sing N N 108 MWB C6 H4 sing N N 109 MWB C7 H5 sing N N 110 MWB C8 H6 sing N N 111 MWB C10 H7 sing N N 112 MWB C12 H8 sing N N 113 MWB N1 H9 sing N N 114 MWB N2 H10 sing N N 115 MWB N5 H15 sing N N 116 MWB N6 H17 sing N N 117 MWB N7 H18 sing N N 118 MWB C15 H19 sing N N 119 MWB C16 H20 sing N N 120 MWB C17 H21 sing N N 121 MWB C17 H22 sing N N 122 MWB C18 H23 sing N N 123 MWB C18 H24 sing N N 124 MWB C15 H11 sing N N 125 MWB C16 H12 sing N N 126 # _ndb_struct_conf_na.entry_id 4OCD _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 B DA 1 1_555 C DT 8 1_555 0.284 -0.125 0.125 7.075 -11.012 1.481 1 B_DA1:DT8_C B 1 ? C 8 ? 20 1 1 B DA 2 1_555 C DT 7 1_555 0.233 -0.150 0.283 4.315 -11.240 -1.461 2 B_DA2:DT7_C B 2 ? C 7 ? 20 1 1 B DA 3 1_555 C DT 6 1_555 0.161 -0.104 0.209 2.828 -17.297 0.296 3 B_DA3:DT6_C B 3 ? C 6 ? 20 1 1 B DA 4 1_555 C DT 5 1_555 -0.342 -0.273 -0.177 -3.618 -15.116 3.696 4 B_DA4:DT5_C B 4 ? C 5 ? 20 1 1 B DT 5 1_555 C DA 4 1_555 -0.178 0.008 -0.069 -0.328 -13.573 2.664 5 B_DT5:DA4_C B 5 ? C 4 ? 20 1 1 B DT 6 1_555 C DA 3 1_555 0.213 -0.382 -0.008 -3.713 -17.184 0.047 6 B_DT6:DA3_C B 6 ? C 3 ? 20 1 1 B DT 7 1_555 C DA 2 1_555 -0.161 -0.044 -0.048 -5.685 -13.314 7.743 7 B_DT7:DA2_C B 7 ? C 2 ? 20 1 1 B DT 8 1_555 C DA 1 1_555 -0.491 -0.195 -0.067 -3.154 -6.197 1.915 8 B_DT8:DA1_C B 8 ? C 1 ? 20 1 1 A DA 1 1_555 A DT 8 12_555 0.187 -0.137 0.041 6.630 -11.172 2.998 9 A_DA1:DT8_A A 1 ? A 8 ? 20 1 1 A DA 2 1_555 A DT 7 12_555 0.124 -0.157 -0.016 4.838 -17.566 1.003 10 A_DA2:DT7_A A 2 ? A 7 ? 20 1 1 A DA 3 1_555 A DT 6 12_555 0.001 -0.065 0.104 3.261 -13.317 -1.584 11 A_DA3:DT6_A A 3 ? A 6 ? 20 1 1 A DA 4 1_555 A DT 5 12_555 0.311 -0.238 0.094 -2.433 -11.064 4.803 12 A_DA4:DT5_A A 4 ? A 5 ? 20 1 1 A DT 5 1_555 A DA 4 12_555 -0.311 -0.238 0.094 2.433 -11.064 4.803 13 A_DT5:DA4_A A 5 ? A 4 ? 20 1 1 A DT 6 1_555 A DA 3 12_555 -0.001 -0.065 0.104 -3.261 -13.317 -1.584 14 A_DT6:DA3_A A 6 ? A 3 ? 20 1 1 A DT 7 1_555 A DA 2 12_555 -0.124 -0.157 -0.016 -4.838 -17.566 1.003 15 A_DT7:DA2_A A 7 ? A 2 ? 20 1 1 A DT 8 1_555 A DA 1 12_555 -0.187 -0.137 0.041 -6.630 -11.172 2.998 16 A_DT8:DA1_A A 8 ? A 1 ? 20 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 B DA 1 1_555 C DT 8 1_555 B DA 2 1_555 C DT 7 1_555 -0.595 0.133 3.384 -2.793 -6.071 39.788 0.905 0.536 3.361 -8.845 4.069 40.322 1 BB_DA1DA2:DT7DT8_CC B 1 ? C 8 ? B 2 ? C 7 ? 1 B DA 2 1_555 C DT 7 1_555 B DA 3 1_555 C DT 6 1_555 -0.118 0.183 3.313 -0.567 -4.370 38.219 0.826 0.107 3.274 -6.647 0.863 38.463 2 BB_DA2DA3:DT6DT7_CC B 2 ? C 7 ? B 3 ? C 6 ? 1 B DA 3 1_555 C DT 6 1_555 B DA 4 1_555 C DT 5 1_555 0.287 0.127 3.369 1.964 -4.378 36.031 0.833 -0.179 3.341 -7.039 -3.157 36.339 3 BB_DA3DA4:DT5DT6_CC B 3 ? C 6 ? B 4 ? C 5 ? 1 B DA 4 1_555 C DT 5 1_555 B DT 5 1_555 C DA 4 1_555 -0.031 -0.226 3.287 -0.769 3.796 32.509 -1.057 -0.077 3.240 6.751 1.368 32.733 4 BB_DA4DT5:DA4DT5_CC B 4 ? C 5 ? B 5 ? C 4 ? 1 B DT 5 1_555 C DA 4 1_555 B DT 6 1_555 C DA 3 1_555 -0.146 0.171 3.288 1.252 -2.059 43.012 0.436 0.323 3.271 -2.806 -1.706 43.076 5 BB_DT5DT6:DA3DA4_CC B 5 ? C 4 ? B 6 ? C 3 ? 1 B DT 6 1_555 C DA 3 1_555 B DT 7 1_555 C DA 2 1_555 0.512 0.064 3.197 3.264 -0.256 33.928 0.149 -0.363 3.231 -0.438 -5.578 34.081 6 BB_DT6DT7:DA2DA3_CC B 6 ? C 3 ? B 7 ? C 2 ? 1 B DT 7 1_555 C DA 2 1_555 B DT 8 1_555 C DA 1 1_555 0.265 0.133 3.128 0.972 -3.112 36.244 0.626 -0.295 3.112 -4.990 -1.559 36.385 7 BB_DT7DT8:DA1DA2_CC B 7 ? C 2 ? B 8 ? C 1 ? 1 A DA 1 1_555 A DT 8 12_555 A DA 2 1_555 A DT 7 12_555 -0.456 0.011 3.297 1.100 -3.919 38.811 0.492 0.816 3.267 -5.878 -1.650 39.016 8 AA_DA1DA2:DT7DT8_AA A 1 ? A 8 ? A 2 ? A 7 ? 1 A DA 2 1_555 A DT 7 12_555 A DA 3 1_555 A DT 6 12_555 -0.144 0.181 3.286 -1.537 -1.514 35.840 0.511 0.013 3.279 -2.457 2.494 35.903 9 AA_DA2DA3:DT6DT7_AA A 2 ? A 7 ? A 3 ? A 6 ? 1 A DA 3 1_555 A DT 6 12_555 A DA 4 1_555 A DT 5 12_555 0.463 0.042 3.425 -1.325 -5.886 41.997 0.684 -0.780 3.374 -8.162 1.837 42.409 10 AA_DA3DA4:DT5DT6_AA A 3 ? A 6 ? A 4 ? A 5 ? 1 A DA 4 1_555 A DT 5 12_555 A DT 5 1_555 A DA 4 12_555 0.000 -0.040 3.299 0.000 1.820 30.074 -0.452 0.000 3.291 3.504 0.000 30.127 11 AA_DA4DT5:DA4DT5_AA A 4 ? A 5 ? A 5 ? A 4 ? 1 A DT 5 1_555 A DA 4 12_555 A DT 6 1_555 A DA 3 12_555 -0.463 0.042 3.425 1.325 -5.886 41.997 0.684 0.780 3.374 -8.162 -1.837 42.409 12 AA_DT5DT6:DA3DA4_AA A 5 ? A 4 ? A 6 ? A 3 ? 1 A DT 6 1_555 A DA 3 12_555 A DT 7 1_555 A DA 2 12_555 0.144 0.181 3.286 1.536 -1.514 35.840 0.511 -0.013 3.279 -2.457 -2.494 35.903 13 AA_DT6DT7:DA2DA3_AA A 6 ? A 3 ? A 7 ? A 2 ? 1 A DT 7 1_555 A DA 2 12_555 A DT 8 1_555 A DA 1 12_555 0.456 0.011 3.297 -1.100 -3.919 38.811 0.492 -0.816 3.267 -5.878 1.650 39.016 14 AA_DT7DT8:DA1DA2_AA A 7 ? A 2 ? A 8 ? A 1 ? # _atom_sites.entry_id 4OCD _atom_sites.fract_transf_matrix[1][1] 0.012818 _atom_sites.fract_transf_matrix[1][2] 0.007401 _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] 0.014801 _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] 0.010923 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P # loop_