data_4H5A # _entry.id 4H5A # _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 4H5A pdb_00004h5a 10.2210/pdb4h5a/pdb NDB NA2024 ? ? RCSB RCSB075036 ? ? WWPDB D_1000075036 ? ? # 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 2012-10-03 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_conn 5 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_conn.pdbx_leaving_atom_flag' 4 2 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 2 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 2 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4H5A _pdbx_database_status.recvd_initial_deposition_date 2012-09-18 _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 ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 4FP6 _pdbx_database_related.details 'Se-DNA without platinum crosslinked' _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Zhang, W.' 1 'Coronado, G.' 2 'Huang, Z.' 3 # _citation.id primary _citation.title 'DNA octamer D (GTseGTACAC) partially crosslinked with platinum' _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Zhang, W.' 1 ? primary 'Coronado, G.' 2 ? primary 'Huang, Z.' 3 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*GP*(2ST)P*GP*GP*CP*CP*AP*C)-3') ; 2520.592 1 ? ? ? 'short DNA 8mer with Se modification' 2 non-polymer syn 'PLATINUM (II) ION' 195.078 1 ? ? ? ? 3 water nat water 18.015 36 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DG)(2ST)(DG)(DG)(DC)(DC)(DA)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GTGGCCAC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'PLATINUM (II) ION' PT 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 2ST n 1 3 DG n 1 4 DG n 1 5 DC n 1 6 DC n 1 7 DA n 1 8 DC 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 2ST 'DNA linking' n ;5-METHYL-2'-SE-METHYL-2'-SELENOURIDINE 5'-(DIHYDROGEN PHOSPHATE) ; ? 'C11 H17 N2 O8 P Se' 415.195 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 HOH non-polymer . WATER ? 'H2 O' 18.015 PT non-polymer . 'PLATINUM (II) ION' ? 'Pt 2' 195.078 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DG 1 1 1 DG G A . n A 1 2 2ST 2 2 2 2ST 2ST A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DG 4 4 4 DG G A . n A 1 5 DC 5 5 5 DC C A . n A 1 6 DC 6 6 6 DC C A . n A 1 7 DA 7 7 7 DA A A . n A 1 8 DC 8 8 8 DC C A . 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 B 2 PT 1 101 1 PT PT A . C 3 HOH 1 201 1 HOH HOH A . C 3 HOH 2 202 2 HOH HOH A . C 3 HOH 3 203 3 HOH HOH A . C 3 HOH 4 204 4 HOH HOH A . C 3 HOH 5 205 5 HOH HOH A . C 3 HOH 6 206 6 HOH HOH A . C 3 HOH 7 207 7 HOH HOH A . C 3 HOH 8 208 8 HOH HOH A . C 3 HOH 9 209 10 HOH HOH A . C 3 HOH 10 210 11 HOH HOH A . C 3 HOH 11 211 14 HOH HOH A . C 3 HOH 12 212 18 HOH HOH A . C 3 HOH 13 213 19 HOH HOH A . C 3 HOH 14 214 20 HOH HOH A . C 3 HOH 15 215 21 HOH HOH A . C 3 HOH 16 216 22 HOH HOH A . C 3 HOH 17 217 23 HOH HOH A . C 3 HOH 18 218 24 HOH HOH A . C 3 HOH 19 219 25 HOH HOH A . C 3 HOH 20 220 26 HOH HOH A . C 3 HOH 21 221 27 HOH HOH A . C 3 HOH 22 222 28 HOH HOH A . C 3 HOH 23 223 29 HOH HOH A . C 3 HOH 24 224 32 HOH HOH A . C 3 HOH 25 225 33 HOH HOH A . C 3 HOH 26 226 35 HOH HOH A . C 3 HOH 27 227 36 HOH HOH A . C 3 HOH 28 228 37 HOH HOH A . C 3 HOH 29 229 39 HOH HOH A . C 3 HOH 30 230 41 HOH HOH A . C 3 HOH 31 231 46 HOH HOH A . C 3 HOH 32 232 47 HOH HOH A . C 3 HOH 33 233 48 HOH HOH A . C 3 HOH 34 234 49 HOH HOH A . C 3 HOH 35 235 50 HOH HOH A . C 3 HOH 36 236 51 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal HKL-2000 'data collection' . ? 1 PHASES phasing . ? 2 REFMAC refinement 5.5.0110 ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # _cell.entry_id 4H5A _cell.length_a 42.310 _cell.length_b 42.310 _cell.length_c 24.310 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _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 4H5A _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4H5A _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 5 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.16 _exptl_crystal.density_percent_sol 43.01 _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 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.8 _exptl_crystal_grow.pdbx_details 'the platinum was added to the crystallization buffer , pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 99 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2012-07-13 _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 0.9795 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ALS BEAMLINE 8.2.2' _diffrn_source.pdbx_synchrotron_site ALS _diffrn_source.pdbx_synchrotron_beamline 8.2.2 _diffrn_source.pdbx_wavelength 0.9795 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 4H5A _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 21.08 _reflns.d_resolution_high 1.42 _reflns.number_obs 4265 _reflns.number_all ? _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs 0.091 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 17.93 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 12.5 _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 # _reflns_shell.d_res_high 1.42 _reflns_shell.d_res_low 1.47 _reflns_shell.percent_possible_all 99.5 _reflns_shell.Rmerge_I_obs 0.584 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.73 _reflns_shell.pdbx_redundancy 9.5 _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 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 4H5A _refine.ls_number_reflns_obs 4265 _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 21.08 _refine.ls_d_res_high 1.42 _refine.ls_percent_reflns_obs 99.25 _refine.ls_R_factor_obs 0.21317 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.21187 _refine.ls_R_factor_R_free 0.23708 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.6 _refine.ls_number_reflns_R_free 206 _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 0.940 _refine.B_iso_mean 19.524 _refine.aniso_B[1][1] -0.02 _refine.aniso_B[2][2] -0.02 _refine.aniso_B[3][3] 0.03 _refine.aniso_B[1][2] 0.00 _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 1.40 _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 0.074 _refine.pdbx_overall_ESU_R_Free 0.074 _refine.overall_SU_ML 0.057 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 1.458 _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 163 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 36 _refine_hist.number_atoms_total 200 _refine_hist.d_res_high 1.42 _refine_hist.d_res_low 21.08 # 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 0.027 0.021 ? 180 ? 'X-RAY DIFFRACTION' r_bond_other_d ? ? ? ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 3.145 3.000 ? 271 ? 'X-RAY DIFFRACTION' r_angle_other_deg ? ? ? ? ? '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 0.437 0.200 ? 32 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.029 0.020 ? 84 ? 'X-RAY DIFFRACTION' r_gen_planes_other ? ? ? ? ? '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 ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcbond_other ? ? ? ? ? 'X-RAY DIFFRACTION' r_mcangle_it ? ? ? ? ? 'X-RAY DIFFRACTION' r_scbond_it 2.456 3.000 ? 180 ? 'X-RAY DIFFRACTION' r_scangle_it 3.151 4.500 ? 271 ? '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 1.418 _refine_ls_shell.d_res_low 1.455 _refine_ls_shell.number_reflns_R_work 293 _refine_ls_shell.R_factor_R_work 0.402 _refine_ls_shell.percent_reflns_obs 96.01 _refine_ls_shell.R_factor_R_free 0.457 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 20 _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 4H5A _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 4H5A _struct.title 'DNA octamer D (GTseGTACAC) partially crosslinked with platinum' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4H5A _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'selenium modification to facilitate crystallization, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4H5A _struct_ref.pdbx_db_accession 4H5A _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4H5A _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 8 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 4H5A _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 8 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 8 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 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)' 2210 ? 1 MORE -30 ? 1 'SSA (A^2)' 2880 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C # 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' 8_554 -y,-x,-z-1/2 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 -12.1550000000 # _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 covale1 covale both ? A DG 1 "O3'" ? ? ? 1_555 A 2ST 2 P ? ? A DG 1 A 2ST 2 1_555 ? ? ? ? ? ? ? 1.625 ? ? covale2 covale both ? A 2ST 2 "O3'" ? ? ? 1_555 A DG 3 P ? ? A 2ST 2 A DG 3 1_555 ? ? ? ? ? ? ? 1.767 ? ? metalc1 metalc ? ? A DG 4 N7 ? ? ? 1_555 B PT . PT ? ? A DG 4 A PT 101 1_555 ? ? ? ? ? ? ? 2.175 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 A DC 8 N3 ? ? A DG 1 A DC 8 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 A DC 8 O2 ? ? A DG 1 A DC 8 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 A DC 8 N4 ? ? A DG 1 A DC 8 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A 2ST 2 N3 ? ? ? 1_555 A DA 7 N1 ? ? A 2ST 2 A DA 7 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A 2ST 2 O4 ? ? ? 1_555 A DA 7 N6 ? ? A 2ST 2 A DA 7 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 3 N1 ? ? ? 1_555 A DC 6 N3 ? ? A DG 3 A DC 6 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DC 6 O2 ? ? A DG 3 A DC 6 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 O6 ? ? ? 1_555 A DC 6 N4 ? ? A DG 3 A DC 6 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N1 ? ? ? 1_555 A DC 5 N3 ? ? A DG 4 A DC 5 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N2 ? ? ? 1_555 A DC 5 O2 ? ? A DG 4 A DC 5 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 O6 ? ? ? 1_555 A DC 5 N4 ? ? A DG 4 A DC 5 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 N3 ? ? ? 1_555 A DG 4 N1 ? ? A DC 5 A DG 4 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 N4 ? ? ? 1_555 A DG 4 O6 ? ? A DC 5 A DG 4 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 5 O2 ? ? ? 1_555 A DG 4 N2 ? ? A DC 5 A DG 4 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 6 N3 ? ? ? 1_555 A DG 3 N1 ? ? A DC 6 A DG 3 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 6 N4 ? ? ? 1_555 A DG 3 O6 ? ? A DC 6 A DG 3 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 6 O2 ? ? ? 1_555 A DG 3 N2 ? ? A DC 6 A DG 3 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DA 7 N1 ? ? ? 1_555 A 2ST 2 N3 ? ? A DA 7 A 2ST 2 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DA 7 N6 ? ? ? 1_555 A 2ST 2 O4 ? ? A DA 7 A 2ST 2 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 N3 ? ? ? 1_555 A DG 1 N1 ? ? A DC 8 A DG 1 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 8 N4 ? ? ? 1_555 A DG 1 O6 ? ? A DC 8 A DG 1 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 8 O2 ? ? ? 1_555 A DG 1 N2 ? ? A DC 8 A DG 1 8_554 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id PT _struct_site.pdbx_auth_seq_id 101 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 2 _struct_site.details 'BINDING SITE FOR RESIDUE PT A 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 2 DG A 4 ? DG A 4 . ? 1_555 ? 2 AC1 2 HOH C . ? HOH A 220 . ? 1_555 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O A HOH 209 ? ? O A HOH 223 ? ? 1.79 2 1 OP2 A DG 3 ? ? O A HOH 231 ? ? 1.94 3 1 O A HOH 222 ? ? O A HOH 223 ? ? 2.00 4 1 O A HOH 227 ? ? O A HOH 231 ? ? 2.11 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 O _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 HOH _pdbx_validate_symm_contact.auth_seq_id_1 224 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 O _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 HOH _pdbx_validate_symm_contact.auth_seq_id_2 232 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 7_655 _pdbx_validate_symm_contact.dist 1.98 # 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 "O3'" A 2ST 2 ? ? P A DG 3 ? ? 1.767 1.607 0.160 0.012 Y 2 1 C5 A DG 3 ? ? N7 A DG 3 ? ? 1.432 1.388 0.044 0.006 N 3 1 N3 A DC 8 ? ? C4 A DC 8 ? ? 1.292 1.335 -0.043 0.007 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 "C5'" A DG 3 ? ? "C4'" A DG 3 ? ? "C3'" A DG 3 ? ? 123.06 115.70 7.36 1.20 N 2 1 "C4'" A DG 3 ? ? "C3'" A DG 3 ? ? "C2'" A DG 3 ? ? 91.87 102.20 -10.33 0.70 N 3 1 "O4'" A DG 3 ? ? "C1'" A DG 3 ? ? N9 A DG 3 ? ? 110.64 108.30 2.34 0.30 N 4 1 N3 A DG 3 ? ? C4 A DG 3 ? ? C5 A DG 3 ? ? 134.02 128.60 5.42 0.50 N 5 1 C5 A DG 3 ? ? N7 A DG 3 ? ? C8 A DG 3 ? ? 100.17 104.30 -4.13 0.50 N 6 1 N7 A DG 3 ? ? C8 A DG 3 ? ? N9 A DG 3 ? ? 117.78 113.10 4.68 0.50 N 7 1 N3 A DG 3 ? ? C4 A DG 3 ? ? N9 A DG 3 ? ? 121.85 126.00 -4.15 0.60 N 8 1 "O4'" A DG 4 ? ? "C4'" A DG 4 ? ? "C3'" A DG 4 ? ? 100.27 104.50 -4.23 0.40 N 9 1 N3 A DC 5 ? ? C2 A DC 5 ? ? O2 A DC 5 ? ? 117.04 121.90 -4.86 0.70 N 10 1 "O4'" A DC 6 ? ? "C4'" A DC 6 ? ? "C3'" A DC 6 ? ? 102.10 104.50 -2.40 0.40 N 11 1 N3 A DC 6 ? ? C4 A DC 6 ? ? C5 A DC 6 ? ? 119.35 121.90 -2.55 0.40 N 12 1 N3 A DC 6 ? ? C2 A DC 6 ? ? O2 A DC 6 ? ? 127.07 121.90 5.17 0.70 N 13 1 "O4'" A DA 7 ? ? "C4'" A DA 7 ? ? "C3'" A DA 7 ? ? 101.56 104.50 -2.94 0.40 N 14 1 C6 A DA 7 ? ? N1 A DA 7 ? ? C2 A DA 7 ? ? 122.78 118.60 4.18 0.60 N 15 1 N1 A DA 7 ? ? C2 A DA 7 ? ? N3 A DA 7 ? ? 125.35 129.30 -3.95 0.50 N 16 1 N9 A DA 7 ? ? C4 A DA 7 ? ? C5 A DA 7 ? ? 103.07 105.80 -2.73 0.40 N 17 1 N1 A DA 7 ? ? C6 A DA 7 ? ? N6 A DA 7 ? ? 123.02 118.60 4.42 0.60 N 18 1 "C4'" A DC 8 ? ? "C3'" A DC 8 ? ? "C2'" A DC 8 ? ? 108.93 103.10 5.83 0.90 N 19 1 N1 A DC 8 ? ? C2 A DC 8 ? ? N3 A DC 8 ? ? 112.52 119.20 -6.68 0.70 N 20 1 C2 A DC 8 ? ? N3 A DC 8 ? ? C4 A DC 8 ? ? 125.37 119.90 5.47 0.50 N 21 1 N3 A DC 8 ? ? C2 A DC 8 ? ? O2 A DC 8 ? ? 126.18 121.90 4.28 0.70 N # _pdbx_validate_polymer_linkage.id 1 _pdbx_validate_polymer_linkage.PDB_model_num 1 _pdbx_validate_polymer_linkage.auth_atom_id_1 "O3'" _pdbx_validate_polymer_linkage.auth_asym_id_1 A _pdbx_validate_polymer_linkage.auth_comp_id_1 2ST _pdbx_validate_polymer_linkage.auth_seq_id_1 2 _pdbx_validate_polymer_linkage.PDB_ins_code_1 ? _pdbx_validate_polymer_linkage.label_alt_id_1 ? _pdbx_validate_polymer_linkage.auth_atom_id_2 P _pdbx_validate_polymer_linkage.auth_asym_id_2 A _pdbx_validate_polymer_linkage.auth_comp_id_2 DG _pdbx_validate_polymer_linkage.auth_seq_id_2 3 _pdbx_validate_polymer_linkage.PDB_ins_code_2 ? _pdbx_validate_polymer_linkage.label_alt_id_2 ? _pdbx_validate_polymer_linkage.dist 1.77 # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id 2ST _pdbx_struct_mod_residue.label_seq_id 2 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id 2ST _pdbx_struct_mod_residue.auth_seq_id 2 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id DT _pdbx_struct_mod_residue.details ? # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 234 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id C _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 2ST OP3 O N N 1 2ST P P N N 2 2ST OP1 O N N 3 2ST OP2 O N N 4 2ST "O5'" O N N 5 2ST N1 N N N 6 2ST C6 C N N 7 2ST C2 C N N 8 2ST O2 O N N 9 2ST N3 N N N 10 2ST C4 C N N 11 2ST O4 O N N 12 2ST C5 C N N 13 2ST C5A C N N 14 2ST "C2'" C N R 15 2ST "C5'" C N N 16 2ST "C4'" C N R 17 2ST "O4'" O N N 18 2ST "C1'" C N R 19 2ST "C3'" C N R 20 2ST SE SE N N 21 2ST "CA'" C N N 22 2ST "O3'" O N N 23 2ST HOP3 H N N 24 2ST HOP2 H N N 25 2ST H6 H N N 26 2ST HN3 H N N 27 2ST H5A1 H N N 28 2ST H5A2 H N N 29 2ST H5A3 H N N 30 2ST "H2'" H N N 31 2ST "H5'" H N N 32 2ST "H5''" H N N 33 2ST "H4'" H N N 34 2ST "H1'" H N N 35 2ST "H3'" H N N 36 2ST "HA'1" H N N 37 2ST "HA'2" H N N 38 2ST "HA'3" H N N 39 2ST "HO3'" H N N 40 DA OP3 O N N 41 DA P P N N 42 DA OP1 O N N 43 DA OP2 O N N 44 DA "O5'" O N N 45 DA "C5'" C N N 46 DA "C4'" C N R 47 DA "O4'" O N N 48 DA "C3'" C N S 49 DA "O3'" O N N 50 DA "C2'" C N N 51 DA "C1'" C N R 52 DA N9 N Y N 53 DA C8 C Y N 54 DA N7 N Y N 55 DA C5 C Y N 56 DA C6 C Y N 57 DA N6 N N N 58 DA N1 N Y N 59 DA C2 C Y N 60 DA N3 N Y N 61 DA C4 C Y N 62 DA HOP3 H N N 63 DA HOP2 H N N 64 DA "H5'" H N N 65 DA "H5''" H N N 66 DA "H4'" H N N 67 DA "H3'" H N N 68 DA "HO3'" H N N 69 DA "H2'" H N N 70 DA "H2''" H N N 71 DA "H1'" H N N 72 DA H8 H N N 73 DA H61 H N N 74 DA H62 H N N 75 DA H2 H N N 76 DC OP3 O N N 77 DC P P N N 78 DC OP1 O N N 79 DC OP2 O N N 80 DC "O5'" O N N 81 DC "C5'" C N N 82 DC "C4'" C N R 83 DC "O4'" O N N 84 DC "C3'" C N S 85 DC "O3'" O N N 86 DC "C2'" C N N 87 DC "C1'" C N R 88 DC N1 N N N 89 DC C2 C N N 90 DC O2 O N N 91 DC N3 N N N 92 DC C4 C N N 93 DC N4 N N N 94 DC C5 C N N 95 DC C6 C N N 96 DC HOP3 H N N 97 DC HOP2 H N N 98 DC "H5'" H N N 99 DC "H5''" H N N 100 DC "H4'" H N N 101 DC "H3'" H N N 102 DC "HO3'" H N N 103 DC "H2'" H N N 104 DC "H2''" H N N 105 DC "H1'" H N N 106 DC H41 H N N 107 DC H42 H N N 108 DC H5 H N N 109 DC H6 H N N 110 DG OP3 O N N 111 DG P P N N 112 DG OP1 O N N 113 DG OP2 O N N 114 DG "O5'" O N N 115 DG "C5'" C N N 116 DG "C4'" C N R 117 DG "O4'" O N N 118 DG "C3'" C N S 119 DG "O3'" O N N 120 DG "C2'" C N N 121 DG "C1'" C N R 122 DG N9 N Y N 123 DG C8 C Y N 124 DG N7 N Y N 125 DG C5 C Y N 126 DG C6 C N N 127 DG O6 O N N 128 DG N1 N N N 129 DG C2 C N N 130 DG N2 N N N 131 DG N3 N N N 132 DG C4 C Y N 133 DG HOP3 H N N 134 DG HOP2 H N N 135 DG "H5'" H N N 136 DG "H5''" H N N 137 DG "H4'" H N N 138 DG "H3'" H N N 139 DG "HO3'" H N N 140 DG "H2'" H N N 141 DG "H2''" H N N 142 DG "H1'" H N N 143 DG H8 H N N 144 DG H1 H N N 145 DG H21 H N N 146 DG H22 H N N 147 HOH O O N N 148 HOH H1 H N N 149 HOH H2 H N N 150 PT PT PT N N 151 # 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 2ST OP3 P sing N N 1 2ST OP3 HOP3 sing N N 2 2ST P OP1 doub N N 3 2ST P OP2 sing N N 4 2ST P "O5'" sing N N 5 2ST OP2 HOP2 sing N N 6 2ST "O5'" "C5'" sing N N 7 2ST N1 C6 sing N N 8 2ST N1 C2 sing N N 9 2ST N1 "C1'" sing N N 10 2ST C6 C5 doub N N 11 2ST C6 H6 sing N N 12 2ST C2 O2 doub N N 13 2ST C2 N3 sing N N 14 2ST N3 C4 sing N N 15 2ST N3 HN3 sing N N 16 2ST C4 O4 doub N N 17 2ST C4 C5 sing N N 18 2ST C5 C5A sing N N 19 2ST C5A H5A1 sing N N 20 2ST C5A H5A2 sing N N 21 2ST C5A H5A3 sing N N 22 2ST "C2'" "C1'" sing N N 23 2ST "C2'" "C3'" sing N N 24 2ST "C2'" SE sing N N 25 2ST "C2'" "H2'" sing N N 26 2ST "C5'" "C4'" sing N N 27 2ST "C5'" "H5'" sing N N 28 2ST "C5'" "H5''" sing N N 29 2ST "C4'" "O4'" sing N N 30 2ST "C4'" "C3'" sing N N 31 2ST "C4'" "H4'" sing N N 32 2ST "O4'" "C1'" sing N N 33 2ST "C1'" "H1'" sing N N 34 2ST "C3'" "O3'" sing N N 35 2ST "C3'" "H3'" sing N N 36 2ST SE "CA'" sing N N 37 2ST "CA'" "HA'1" sing N N 38 2ST "CA'" "HA'2" sing N N 39 2ST "CA'" "HA'3" sing N N 40 2ST "O3'" "HO3'" sing N N 41 DA OP3 P sing N N 42 DA OP3 HOP3 sing N N 43 DA P OP1 doub N N 44 DA P OP2 sing N N 45 DA P "O5'" sing N N 46 DA OP2 HOP2 sing N N 47 DA "O5'" "C5'" sing N N 48 DA "C5'" "C4'" sing N N 49 DA "C5'" "H5'" sing N N 50 DA "C5'" "H5''" sing N N 51 DA "C4'" "O4'" sing N N 52 DA "C4'" "C3'" sing N N 53 DA "C4'" "H4'" sing N N 54 DA "O4'" "C1'" sing N N 55 DA "C3'" "O3'" sing N N 56 DA "C3'" "C2'" sing N N 57 DA "C3'" "H3'" sing N N 58 DA "O3'" "HO3'" sing N N 59 DA "C2'" "C1'" sing N N 60 DA "C2'" "H2'" sing N N 61 DA "C2'" "H2''" sing N N 62 DA "C1'" N9 sing N N 63 DA "C1'" "H1'" sing N N 64 DA N9 C8 sing Y N 65 DA N9 C4 sing Y N 66 DA C8 N7 doub Y N 67 DA C8 H8 sing N N 68 DA N7 C5 sing Y N 69 DA C5 C6 sing Y N 70 DA C5 C4 doub Y N 71 DA C6 N6 sing N N 72 DA C6 N1 doub Y N 73 DA N6 H61 sing N N 74 DA N6 H62 sing N N 75 DA N1 C2 sing Y N 76 DA C2 N3 doub Y N 77 DA C2 H2 sing N N 78 DA N3 C4 sing Y N 79 DC OP3 P sing N N 80 DC OP3 HOP3 sing N N 81 DC P OP1 doub N N 82 DC P OP2 sing N N 83 DC P "O5'" sing N N 84 DC OP2 HOP2 sing N N 85 DC "O5'" "C5'" sing N N 86 DC "C5'" "C4'" sing N N 87 DC "C5'" "H5'" sing N N 88 DC "C5'" "H5''" sing N N 89 DC "C4'" "O4'" sing N N 90 DC "C4'" "C3'" sing N N 91 DC "C4'" "H4'" sing N N 92 DC "O4'" "C1'" sing N N 93 DC "C3'" "O3'" sing N N 94 DC "C3'" "C2'" sing N N 95 DC "C3'" "H3'" sing N N 96 DC "O3'" "HO3'" sing N N 97 DC "C2'" "C1'" sing N N 98 DC "C2'" "H2'" sing N N 99 DC "C2'" "H2''" sing N N 100 DC "C1'" N1 sing N N 101 DC "C1'" "H1'" sing N N 102 DC N1 C2 sing N N 103 DC N1 C6 sing N N 104 DC C2 O2 doub N N 105 DC C2 N3 sing N N 106 DC N3 C4 doub N N 107 DC C4 N4 sing N N 108 DC C4 C5 sing N N 109 DC N4 H41 sing N N 110 DC N4 H42 sing N N 111 DC C5 C6 doub N N 112 DC C5 H5 sing N N 113 DC C6 H6 sing N N 114 DG OP3 P sing N N 115 DG OP3 HOP3 sing N N 116 DG P OP1 doub N N 117 DG P OP2 sing N N 118 DG P "O5'" sing N N 119 DG OP2 HOP2 sing N N 120 DG "O5'" "C5'" sing N N 121 DG "C5'" "C4'" sing N N 122 DG "C5'" "H5'" sing N N 123 DG "C5'" "H5''" sing N N 124 DG "C4'" "O4'" sing N N 125 DG "C4'" "C3'" sing N N 126 DG "C4'" "H4'" sing N N 127 DG "O4'" "C1'" sing N N 128 DG "C3'" "O3'" sing N N 129 DG "C3'" "C2'" sing N N 130 DG "C3'" "H3'" sing N N 131 DG "O3'" "HO3'" sing N N 132 DG "C2'" "C1'" sing N N 133 DG "C2'" "H2'" sing N N 134 DG "C2'" "H2''" sing N N 135 DG "C1'" N9 sing N N 136 DG "C1'" "H1'" sing N N 137 DG N9 C8 sing Y N 138 DG N9 C4 sing Y N 139 DG C8 N7 doub Y N 140 DG C8 H8 sing N N 141 DG N7 C5 sing Y N 142 DG C5 C6 sing N N 143 DG C5 C4 doub Y N 144 DG C6 O6 doub N N 145 DG C6 N1 sing N N 146 DG N1 C2 sing N N 147 DG N1 H1 sing N N 148 DG C2 N2 sing N N 149 DG C2 N3 doub N N 150 DG N2 H21 sing N N 151 DG N2 H22 sing N N 152 DG N3 C4 sing N N 153 HOH O H1 sing N N 154 HOH O H2 sing N N 155 # _ndb_struct_conf_na.entry_id 4H5A _ndb_struct_conf_na.feature 'a-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 DG 1 1_555 A DC 8 8_554 -0.381 -0.011 -0.355 -20.786 -9.164 1.784 1 A_DG1:DC8_A A 1 ? A 8 ? 19 1 1 A 2ST 2 1_555 A DA 7 8_554 -0.169 -0.105 0.126 -7.576 -12.387 -1.021 2 A_2ST2:DA7_A A 2 ? A 7 ? 20 1 1 A DG 3 1_555 A DC 6 8_554 -0.220 -0.218 0.134 -5.038 -11.692 -1.523 3 A_DG3:DC6_A A 3 ? A 6 ? 19 1 1 A DG 4 1_555 A DC 5 8_554 -0.176 -0.079 0.099 -5.367 -14.376 -0.746 4 A_DG4:DC5_A A 4 ? A 5 ? 19 1 1 A DC 5 1_555 A DG 4 8_554 0.176 -0.079 0.099 5.367 -14.375 -0.746 5 A_DC5:DG4_A A 5 ? A 4 ? 19 1 1 A DC 6 1_555 A DG 3 8_554 0.220 -0.218 0.134 5.038 -11.692 -1.523 6 A_DC6:DG3_A A 6 ? A 3 ? 19 1 1 A DA 7 1_555 A 2ST 2 8_554 0.169 -0.105 0.126 7.576 -12.387 -1.021 7 A_DA7:2ST2_A A 7 ? A 2 ? 20 1 1 A DC 8 1_555 A DG 1 8_554 0.381 -0.011 -0.355 20.786 -9.164 1.784 8 A_DC8:DG1_A A 8 ? A 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 DG 1 1_555 A DC 8 8_554 A 2ST 2 1_555 A DA 7 8_554 -0.047 -1.014 3.074 -2.722 9.366 31.136 -3.270 -0.342 2.660 16.935 4.922 32.592 1 AA_DG12ST2:DA7DC8_AA A 1 ? A 8 ? A 2 ? A 7 ? 1 A 2ST 2 1_555 A DA 7 8_554 A DG 3 1_555 A DC 6 8_554 0.599 -1.409 3.143 1.423 9.093 29.102 -4.314 -0.883 2.619 17.549 -2.747 30.493 2 AA_2ST2DG3:DC6DA7_AA A 2 ? A 7 ? A 3 ? A 6 ? 1 A DG 3 1_555 A DC 6 8_554 A DG 4 1_555 A DC 5 8_554 0.375 -1.701 3.224 2.924 5.948 35.261 -3.572 -0.211 2.928 9.713 -4.774 35.859 3 AA_DG3DG4:DC5DC6_AA A 3 ? A 6 ? A 4 ? A 5 ? 1 A DG 4 1_555 A DC 5 8_554 A DC 5 1_555 A DG 4 8_554 0.000 -1.061 3.111 0.000 4.588 29.187 -2.984 0.000 2.914 9.034 0.000 29.538 4 AA_DG4DC5:DG4DC5_AA A 4 ? A 5 ? A 5 ? A 4 ? 1 A DC 5 1_555 A DG 4 8_554 A DC 6 1_555 A DG 3 8_554 -0.375 -1.701 3.224 -2.924 5.948 35.261 -3.572 0.211 2.928 9.713 4.774 35.859 5 AA_DC5DC6:DG3DG4_AA A 5 ? A 4 ? A 6 ? A 3 ? 1 A DC 6 1_555 A DG 3 8_554 A DA 7 1_555 A 2ST 2 8_554 -0.599 -1.409 3.143 -1.423 9.093 29.102 -4.314 0.883 2.619 17.549 2.747 30.493 6 AA_DC6DA7:2ST2DG3_AA A 6 ? A 3 ? A 7 ? A 2 ? 1 A DA 7 1_555 A 2ST 2 8_554 A DC 8 1_555 A DG 1 8_554 0.047 -1.014 3.074 2.722 9.366 31.136 -3.270 0.342 2.660 16.935 -4.922 32.592 7 AA_DA7DC8:DG12ST2_AA A 7 ? A 2 ? A 8 ? A 1 ? # _atom_sites.entry_id 4H5A _atom_sites.fract_transf_matrix[1][1] 0.023635 _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] 0.023635 _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] 0.041135 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P PT SE # loop_