data_8XP8 # _entry.id 8XP8 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.395 _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 8XP8 pdb_00008xp8 10.2210/pdb8xp8/pdb WWPDB D_1300043911 ? ? # 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 2024-05-29 2 'Structure model' 1 1 2024-08-14 3 'Structure model' 1 2 2024-08-28 # _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' 'Database references' 2 3 'Structure model' 'Database references' # 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' citation 2 2 'Structure model' citation_author 3 3 'Structure model' citation 4 3 'Structure model' citation_author # 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' '_citation.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_id_ASTM' 4 2 'Structure model' '_citation.journal_id_CSD' 5 2 'Structure model' '_citation.journal_id_ISSN' 6 2 'Structure model' '_citation.pdbx_database_id_DOI' 7 2 'Structure model' '_citation.pdbx_database_id_PubMed' 8 2 'Structure model' '_citation.title' 9 2 'Structure model' '_citation.year' 10 3 'Structure model' '_citation.journal_volume' 11 3 'Structure model' '_citation.page_first' 12 3 'Structure model' '_citation.page_last' 13 3 'Structure model' '_citation_author.identifier_ORCID' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8XP8 _pdbx_database_status.recvd_initial_deposition_date 2024-01-03 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_contact_author.id 2 _pdbx_contact_author.email mhho@dragon.nchu.edu.tw _pdbx_contact_author.name_first Ming-Hon _pdbx_contact_author.name_last Hou _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0003-4170-1527 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Hou, M.H.' 1 0000-0003-4170-1527 'Lin, S.M.' 2 0000-0001-7813-9000 'Neidle, H.' 3 0000-0003-0622-6548 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_id_ASTM NARHAD _citation.journal_id_CSD 0389 _citation.journal_id_ISSN 1362-4962 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 52 _citation.language ? _citation.page_first 8566 _citation.page_last 8579 _citation.title 'Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation.' _citation.year 2024 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1093/nar/gkae594 _citation.pdbx_database_id_PubMed 38989613 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Lin, S.M.' 1 ? primary 'Huang, H.T.' 2 ? primary 'Fang, P.J.' 3 ? primary 'Chang, C.F.' 4 ? primary 'Satange, R.' 5 ? primary 'Chang, C.K.' 6 ? primary 'Chou, S.H.' 7 ? primary 'Neidle, S.' 8 ? primary 'Hou, M.H.' 9 ? # 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(P*AP*CP*GP*GP*CP*GP*T)-3') ; 2138.423 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(P*AP*CP*GP*(5CM)P*CP*GP*T)-3') ; 2112.426 1 ? ? ? ? 3 polymer nat Echinomycin 809.008 2 ? ? ? ? 4 non-polymer syn 'MANGANESE (II) ION' 54.938 3 ? ? ? ? 5 non-polymer syn 2-CARBOXYQUINOXALINE 174.156 4 ? ? ? ? 6 water nat water 18.015 47 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no no '(DA)(DC)(DG)(DG)(DC)(DG)(DT)' ACGGCGT A ? 2 polydeoxyribonucleotide no yes '(DA)(DC)(DG)(5CM)(DC)(DG)(DT)' ACGCCGT B ? 3 'polypeptide(L)' no yes '(DSN)A(N2C)(MVA)(DSN)A(NCY)(MVA)' SAXVSAXV D,E ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 4 'MANGANESE (II) ION' MN 5 2-CARBOXYQUINOXALINE QUI 6 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 DC n 1 3 DG n 1 4 DG n 1 5 DC n 1 6 DG n 1 7 DT n 2 1 DA n 2 2 DC n 2 3 DG n 2 4 5CM n 2 5 DC n 2 6 DG n 2 7 DT n 3 1 DSN n 3 2 ALA n 3 3 N2C n 3 4 MVA n 3 5 DSN n 3 6 ALA n 3 7 NCY n 3 8 MVA n # _entity_src_nat.entity_id 3 _entity_src_nat.pdbx_src_id 1 _entity_src_nat.pdbx_alt_source_flag sample _entity_src_nat.pdbx_beg_seq_num 1 _entity_src_nat.pdbx_end_seq_num 8 _entity_src_nat.common_name ? _entity_src_nat.pdbx_organism_scientific 'Streptomyces echinatus.' _entity_src_nat.pdbx_ncbi_taxonomy_id 67293 _entity_src_nat.genus ? _entity_src_nat.species ? _entity_src_nat.strain ? _entity_src_nat.tissue ? _entity_src_nat.tissue_fraction ? _entity_src_nat.pdbx_secretion ? _entity_src_nat.pdbx_fragment ? _entity_src_nat.pdbx_variant ? _entity_src_nat.pdbx_cell_line ? _entity_src_nat.pdbx_atcc ? _entity_src_nat.pdbx_cellular_location ? _entity_src_nat.pdbx_organ ? _entity_src_nat.pdbx_organelle ? _entity_src_nat.pdbx_cell ? _entity_src_nat.pdbx_plasmid_name ? _entity_src_nat.pdbx_plasmid_details ? _entity_src_nat.details ? # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample 1 7 'synthetic construct' ? 32630 ? 2 1 sample 1 7 'synthetic construct' ? 32630 ? # 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 5CM 'DNA linking' n "5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C10 H16 N3 O7 P' 321.224 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 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 DSN 'D-peptide linking' . D-SERINE ? 'C3 H7 N O3' 105.093 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 MN non-polymer . 'MANGANESE (II) ION' ? 'Mn 2' 54.938 MVA 'L-peptide linking' n N-METHYLVALINE ? 'C6 H13 N O2' 131.173 N2C 'L-peptide linking' . N,S-DIMETHYLCYSTEINE ? 'C5 H11 N O2 S' 149.211 NCY 'L-peptide linking' . N-METHYLCYSTEINE ? 'C4 H9 N O2 S' 135.185 QUI non-polymer . 2-CARBOXYQUINOXALINE ? 'C9 H6 N2 O2' 174.156 # 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 DC 2 2 2 DC DC A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DC 5 5 5 DC DC A . n A 1 6 DG 6 6 6 DG DG A . n A 1 7 DT 7 7 7 DT DT A . n B 2 1 DA 1 1 1 DA DA B . n B 2 2 DC 2 2 2 DC DC B . n B 2 3 DG 3 3 3 DG DG B . n B 2 4 5CM 4 4 4 5CM 5MC B . n B 2 5 DC 5 5 5 DC DC B . n B 2 6 DG 6 6 6 DG DG B . n B 2 7 DT 7 7 7 DT DT B . n C 3 1 DSN 1 1 8 DSN LIG D . n C 3 2 ALA 2 2 8 ALA LIG D . n C 3 3 N2C 3 3 8 N2C LIG D . n C 3 4 MVA 4 4 8 MVA LIG D . n C 3 5 DSN 5 5 8 DSN LIG D . n C 3 6 ALA 6 6 8 ALA LIG D . n C 3 7 NCY 7 7 8 NCY LIG D . n C 3 8 MVA 8 8 8 MVA LIG D . n D 3 1 DSN 1 1 9 DSN LIG E . n D 3 2 ALA 2 2 9 ALA LIG E . n D 3 3 N2C 3 3 9 N2C LIG E . n D 3 4 MVA 4 4 9 MVA LIG E . n D 3 5 DSN 5 5 9 DSN LIG E . n D 3 6 ALA 6 6 9 ALA LIG E . n D 3 7 NCY 7 7 9 NCY LIG E . n D 3 8 MVA 8 8 9 MVA LIG E . 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 E 4 MN 1 101 1 MN MN A . F 4 MN 1 102 2 MN MN A . G 4 MN 1 101 37 MN MN B . H 5 QUI 1 101 8 QUI LIG D . I 5 QUI 1 102 8 QUI LIG D . J 5 QUI 1 101 9 QUI LIG E . K 5 QUI 1 102 9 QUI LIG E . L 6 HOH 1 201 1 HOH HOH A . L 6 HOH 2 202 19 HOH HOH A . L 6 HOH 3 203 13 HOH HOH A . L 6 HOH 4 204 50 HOH HOH A . L 6 HOH 5 205 12 HOH HOH A . L 6 HOH 6 206 7 HOH HOH A . L 6 HOH 7 207 4 HOH HOH A . L 6 HOH 8 208 15 HOH HOH A . L 6 HOH 9 209 14 HOH HOH A . L 6 HOH 10 210 20 HOH HOH A . L 6 HOH 11 211 16 HOH HOH A . L 6 HOH 12 212 22 HOH HOH A . L 6 HOH 13 213 11 HOH HOH A . L 6 HOH 14 214 18 HOH HOH A . L 6 HOH 15 215 24 HOH HOH A . L 6 HOH 16 216 5 HOH HOH A . L 6 HOH 17 217 10 HOH HOH A . L 6 HOH 18 218 9 HOH HOH A . L 6 HOH 19 219 25 HOH HOH A . L 6 HOH 20 220 17 HOH HOH A . L 6 HOH 21 221 3 HOH HOH A . L 6 HOH 22 222 21 HOH HOH A . L 6 HOH 23 223 57 HOH HOH A . L 6 HOH 24 224 26 HOH HOH A . M 6 HOH 1 201 52 HOH HOH B . M 6 HOH 2 202 45 HOH HOH B . M 6 HOH 3 203 46 HOH HOH B . M 6 HOH 4 204 56 HOH HOH B . M 6 HOH 5 205 3 HOH HOH B . M 6 HOH 6 206 42 HOH HOH B . M 6 HOH 7 207 49 HOH HOH B . M 6 HOH 8 208 39 HOH HOH B . M 6 HOH 9 209 48 HOH HOH B . M 6 HOH 10 210 43 HOH HOH B . M 6 HOH 11 211 2 HOH HOH B . M 6 HOH 12 212 54 HOH HOH B . M 6 HOH 13 213 38 HOH HOH B . M 6 HOH 14 214 40 HOH HOH B . M 6 HOH 15 215 44 HOH HOH B . M 6 HOH 16 216 51 HOH HOH B . M 6 HOH 17 217 47 HOH HOH B . M 6 HOH 18 218 55 HOH HOH B . M 6 HOH 19 219 53 HOH HOH B . N 6 HOH 1 201 6 HOH HOH D . N 6 HOH 2 202 23 HOH HOH D . O 6 HOH 1 201 41 HOH HOH E . O 6 HOH 2 202 27 HOH HOH E . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? '(1.20.1_4487: ???)' 1 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 2 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 4 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 120.00 _cell.angle_gamma_esd ? _cell.entry_id 8XP8 _cell.details ? _cell.formula_units_Z ? _cell.length_a 46.329 _cell.length_a_esd ? _cell.length_b 46.329 _cell.length_b_esd ? _cell.length_c 47.954 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 12 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 8XP8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 151 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 1 2' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 8XP8 _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 2.52 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 51.28 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '20mM MES (pH 6), 5mM Spermine HCl, 1.2% PEG 200, 10mM MnCl2' _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 293.15 # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'RAYONIX MX300-HS' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2021-10-16 _diffrn_detector.pdbx_frequency ? _diffrn_detector.id ? _diffrn_detector.number_of_axes ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.99984 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'NSRRC BEAMLINE TPS 05A' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.99984 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 'TPS 05A' _diffrn_source.pdbx_synchrotron_site NSRRC # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 8XP8 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.64 _reflns.d_resolution_low 30.00 _reflns.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.number_all ? _reflns.number_obs 7315 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 98.9 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 10.8 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 17.0 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs 0.055 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_CC_split_method ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_CC_star _reflns_shell.pdbx_R_split _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_percent_possible_ellipsoidal _reflns_shell.pdbx_percent_possible_spherical _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous _reflns_shell.pdbx_percent_possible_spherical_anomalous _reflns_shell.pdbx_redundancy_anomalous _reflns_shell.pdbx_CC_half_anomalous _reflns_shell.pdbx_absDiff_over_sigma_anomalous _reflns_shell.pdbx_percent_possible_anomalous 1.64 1.70 ? ? ? ? ? ? 721 ? ? ? ? ? ? ? ? ? ? ? 10.7 1.033 ? ? 0.120 0.038 ? 1 1 0.999 1.000 ? 100.0 ? 0.114 ? ? ? ? ? ? ? ? ? 1.70 1.77 ? ? ? ? ? ? 735 ? ? ? ? ? ? ? ? ? ? ? 11.0 1.038 ? ? 0.124 0.038 ? 2 1 0.999 1.000 ? 100.0 ? 0.118 ? ? ? ? ? ? ? ? ? 1.77 1.85 ? ? ? ? ? ? 727 ? ? ? ? ? ? ? ? ? ? ? 11.0 1.061 ? ? 0.108 0.033 ? 3 1 0.998 1.000 ? 100.0 ? 0.102 ? ? ? ? ? ? ? ? ? 1.85 1.94 ? ? ? ? ? ? 736 ? ? ? ? ? ? ? ? ? ? ? 11.1 1.048 ? ? 0.097 0.029 ? 4 1 0.998 1.000 ? 100.0 ? 0.092 ? ? ? ? ? ? ? ? ? 1.94 2.07 ? ? ? ? ? ? 724 ? ? ? ? ? ? ? ? ? ? ? 11.1 1.029 ? ? 0.086 0.026 ? 5 1 0.997 0.999 ? 100.0 ? 0.081 ? ? ? ? ? ? ? ? ? 2.07 2.23 ? ? ? ? ? ? 757 ? ? ? ? ? ? ? ? ? ? ? 11.1 1.072 ? ? 0.076 0.023 ? 6 1 0.998 1.000 ? 100.0 ? 0.073 ? ? ? ? ? ? ? ? ? 2.23 2.45 ? ? ? ? ? ? 727 ? ? ? ? ? ? ? ? ? ? ? 11.1 1.059 ? ? 0.061 0.018 ? 7 1 0.999 1.000 ? 100.0 ? 0.058 ? ? ? ? ? ? ? ? ? 2.45 2.80 ? ? ? ? ? ? 735 ? ? ? ? ? ? ? ? ? ? ? 10.9 1.095 ? ? 0.061 0.019 ? 8 1 0.999 1.000 ? 100.0 ? 0.058 ? ? ? ? ? ? ? ? ? 2.80 3.53 ? ? ? ? ? ? 729 ? ? ? ? ? ? ? ? ? ? ? 10.5 0.959 ? ? 0.056 0.018 ? 9 1 0.999 1.000 ? 97.1 ? 0.053 ? ? ? ? ? ? ? ? ? 3.53 30.00 ? ? ? ? ? ? 724 ? ? ? ? ? ? ? ? ? ? ? 9.5 1.026 ? ? 0.052 0.017 ? 10 1 0.998 0.999 ? 92.3 ? 0.048 ? ? ? ? ? ? ? ? ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean ? _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 8XP8 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.64 _refine.ls_d_res_low 16.66 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 7240 _refine.ls_number_reflns_R_free 716 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 98.21 _refine.ls_percent_reflns_R_free 9.89 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2348 _refine.ls_R_factor_R_free 0.2428 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2339 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.41 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method NONE _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.10 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 32.31 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.18 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.details ? _refine_hist.d_res_high 1.64 _refine_hist.d_res_low 16.66 _refine_hist.number_atoms_solvent 47 _refine_hist.number_atoms_total 486 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 282 _refine_hist.pdbx_number_atoms_ligand 157 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.018 ? ? ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 2.475 ? ? ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 32.400 ? 186 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.151 ? 86 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.010 ? 42 ? f_plane_restr ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free _refine_ls_shell.R_factor_R_free 'X-RAY DIFFRACTION' 1.64 1.77 . . 145 1285 98.00 . . . . 0.2720 . . . . . . . . . . . 0.2942 'X-RAY DIFFRACTION' 1.77 1.94 . . 135 1308 99.00 . . . . 0.2899 . . . . . . . . . . . 0.3143 'X-RAY DIFFRACTION' 1.94 2.22 . . 148 1322 100.00 . . . . 0.3016 . . . . . . . . . . . 0.3490 'X-RAY DIFFRACTION' 2.22 2.80 . . 143 1314 100.00 . . . . 0.2554 . . . . . . . . . . . 0.2702 'X-RAY DIFFRACTION' 2.80 10 . . 145 1295 95.00 . . . . 0.1961 . . . . . . . . . . . 0.1961 # _struct.entry_id 8XP8 _struct.title 'Crystal structure of d(ACGmCCGT/ACGGCGT) in complex with Echinomycin' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 8XP8 _struct_keywords.text 'DNA-ligand Complex, DNA, Antibiotic, DNA-ANTIBIOTIC complex' _struct_keywords.pdbx_keywords DNA/ANTIBIOTIC # 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 ? D N N 3 ? E N N 4 ? F N N 4 ? G N N 4 ? H N N 5 ? I N N 5 ? J N N 5 ? K N N 5 ? L N N 6 ? M N N 6 ? N N N 6 ? O N N 6 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 PDB 8XP8 8XP8 ? 1 ? 1 2 PDB 8XP8 8XP8 ? 2 ? 1 3 PDB 8XP8 8XP8 ? 3 ? 1 # 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 8XP8 A 1 ? 7 ? 8XP8 1 ? 7 ? 1 7 2 2 8XP8 B 1 ? 7 ? 8XP8 1 ? 7 ? 1 7 3 3 8XP8 D 1 ? 8 ? 8XP8 1 ? 8 ? 1 8 4 3 8XP8 E 1 ? 8 ? 8XP8 1 ? 8 ? 1 8 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role disulf1 disulf ? ? C N2C 3 SG ? ? ? 1_555 C NCY 7 SG ? ? D N2C 3 D NCY 7 1_555 ? ? ? ? ? ? ? 2.912 ? ? disulf2 disulf ? ? D N2C 3 SG ? ? ? 1_555 D NCY 7 SG ? ? E N2C 3 E NCY 7 1_555 ? ? ? ? ? ? ? 2.827 ? ? covale1 covale both ? B DG 3 "O3'" ? ? ? 1_555 B 5CM 4 P A ? B DG 3 B 5CM 4 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale2 covale both ? B DG 3 "O3'" ? ? ? 1_555 B 5CM 4 P B ? B DG 3 B 5CM 4 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale3 covale both ? B 5CM 4 "O3'" A ? ? 1_555 B DC 5 P ? ? B 5CM 4 B DC 5 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale4 covale both ? B 5CM 4 "O3'" B ? ? 1_555 B DC 5 P ? ? B 5CM 4 B DC 5 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale5 covale both ? C DSN 1 C ? ? ? 1_555 C ALA 2 N ? ? D DSN 1 D ALA 2 1_555 ? ? ? ? ? ? ? 1.463 ? ? covale6 covale one ? C DSN 1 OG ? ? ? 1_555 C MVA 8 C ? ? D DSN 1 D MVA 8 1_555 ? ? ? ? ? ? ? 1.429 ? ? covale7 covale both ? C DSN 1 N ? ? ? 1_555 H QUI . C ? ? D DSN 1 D QUI 101 1_555 ? ? ? ? ? ? ? 1.481 ? ? covale8 covale both ? C ALA 2 C ? ? ? 1_555 C N2C 3 N ? ? D ALA 2 D N2C 3 1_555 ? ? ? ? ? ? ? 1.494 ? ? covale9 covale both ? C N2C 3 C ? ? ? 1_555 C MVA 4 N ? ? D N2C 3 D MVA 4 1_555 ? ? ? ? ? ? ? 1.506 ? ? covale10 covale both ? C N2C 3 CB ? ? ? 1_555 C NCY 7 SG ? ? D N2C 3 D NCY 7 1_555 ? ? ? ? ? ? ? 1.829 ? ? covale11 covale one ? C MVA 4 C ? ? ? 1_555 C DSN 5 OG ? ? D MVA 4 D DSN 5 1_555 ? ? ? ? ? ? ? 1.393 ? ? covale12 covale both ? C DSN 5 C ? ? ? 1_555 C ALA 6 N ? ? D DSN 5 D ALA 6 1_555 ? ? ? ? ? ? ? 1.452 ? ? covale13 covale both ? C DSN 5 N ? ? ? 1_555 I QUI . C ? ? D DSN 5 D QUI 102 1_555 ? ? ? ? ? ? ? 1.475 ? ? covale14 covale both ? C ALA 6 C ? ? ? 1_555 C NCY 7 N ? ? D ALA 6 D NCY 7 1_555 ? ? ? ? ? ? ? 1.477 ? ? covale15 covale both ? C NCY 7 C ? ? ? 1_555 C MVA 8 N ? ? D NCY 7 D MVA 8 1_555 ? ? ? ? ? ? ? 1.501 ? ? covale16 covale both ? D DSN 1 C ? ? ? 1_555 D ALA 2 N ? ? E DSN 1 E ALA 2 1_555 ? ? ? ? ? ? ? 1.470 ? ? covale17 covale one ? D DSN 1 OG ? ? ? 1_555 D MVA 8 C ? ? E DSN 1 E MVA 8 1_555 ? ? ? ? ? ? ? 1.413 ? ? covale18 covale both ? D DSN 1 N ? ? ? 1_555 J QUI . C ? ? E DSN 1 E QUI 101 1_555 ? ? ? ? ? ? ? 1.463 ? ? covale19 covale both ? D ALA 2 C ? ? ? 1_555 D N2C 3 N ? ? E ALA 2 E N2C 3 1_555 ? ? ? ? ? ? ? 1.479 ? ? covale20 covale both ? D N2C 3 C ? ? ? 1_555 D MVA 4 N ? ? E N2C 3 E MVA 4 1_555 ? ? ? ? ? ? ? 1.498 ? ? covale21 covale both ? D N2C 3 CB ? ? ? 1_555 D NCY 7 SG ? ? E N2C 3 E NCY 7 1_555 ? ? ? ? ? ? ? 1.826 ? ? covale22 covale one ? D MVA 4 C ? ? ? 1_555 D DSN 5 OG ? ? E MVA 4 E DSN 5 1_555 ? ? ? ? ? ? ? 1.376 ? ? covale23 covale both ? D DSN 5 C ? ? ? 1_555 D ALA 6 N ? ? E DSN 5 E ALA 6 1_555 ? ? ? ? ? ? ? 1.452 ? ? covale24 covale both ? D DSN 5 N ? ? ? 1_555 K QUI . C ? ? E DSN 5 E QUI 102 1_555 ? ? ? ? ? ? ? 1.473 ? ? covale25 covale both ? D ALA 6 C ? ? ? 1_555 D NCY 7 N ? ? E ALA 6 E NCY 7 1_555 ? ? ? ? ? ? ? 1.473 ? ? covale26 covale both ? D NCY 7 C ? ? ? 1_555 D MVA 8 N ? ? E NCY 7 E MVA 8 1_555 ? ? ? ? ? ? ? 1.492 ? ? metalc1 metalc ? ? A DG 3 N7 ? ? ? 1_555 F MN . MN ? ? A DG 3 A MN 102 1_555 ? ? ? ? ? ? ? 2.221 ? ? metalc2 metalc ? ? A DG 6 N7 ? ? ? 1_555 E MN . MN ? ? A DG 6 A MN 101 1_555 ? ? ? ? ? ? ? 2.303 ? ? metalc3 metalc ? ? E MN . MN ? ? ? 1_555 L HOH . O ? ? A MN 101 A HOH 208 1_555 ? ? ? ? ? ? ? 2.532 ? ? metalc4 metalc ? ? E MN . MN ? ? ? 1_555 L HOH . O ? ? A MN 101 A HOH 212 1_555 ? ? ? ? ? ? ? 2.249 ? ? metalc5 metalc ? ? E MN . MN ? ? ? 1_555 L HOH . O ? ? A MN 101 A HOH 215 1_555 ? ? ? ? ? ? ? 2.366 ? ? metalc6 metalc ? ? E MN . MN ? ? ? 1_555 L HOH . O ? ? A MN 101 A HOH 217 1_555 ? ? ? ? ? ? ? 2.214 ? ? metalc7 metalc ? ? E MN . MN ? ? ? 1_555 L HOH . O ? ? A MN 101 A HOH 224 1_555 ? ? ? ? ? ? ? 2.463 ? ? metalc8 metalc ? ? F MN . MN ? ? ? 1_555 L HOH . O ? ? A MN 102 A HOH 207 1_555 ? ? ? ? ? ? ? 2.275 ? ? metalc9 metalc ? ? F MN . MN ? ? ? 1_555 L HOH . O ? ? A MN 102 A HOH 216 1_555 ? ? ? ? ? ? ? 2.284 ? ? metalc10 metalc ? ? F MN . MN ? ? ? 6_557 B DG 3 N7 ? ? A MN 102 B DG 3 1_555 ? ? ? ? ? ? ? 2.250 ? ? metalc11 metalc ? ? F MN . MN ? ? ? 1_555 M HOH . O ? ? A MN 102 B HOH 205 6_557 ? ? ? ? ? ? ? 2.242 ? ? metalc12 metalc ? ? F MN . MN ? ? ? 1_555 M HOH . O ? ? A MN 102 B HOH 213 6_557 ? ? ? ? ? ? ? 2.299 ? ? metalc13 metalc ? ? B DG 6 N7 ? ? ? 1_555 G MN . MN ? ? B DG 6 B MN 101 1_555 ? ? ? ? ? ? ? 2.211 ? ? metalc14 metalc ? ? G MN . MN ? ? ? 1_555 M HOH . O ? ? B MN 101 B HOH 212 1_555 ? ? ? ? ? ? ? 2.264 ? ? metalc15 metalc ? ? G MN . MN ? ? ? 1_555 M HOH . O ? ? B MN 101 B HOH 215 1_555 ? ? ? ? ? ? ? 2.217 ? ? metalc16 metalc ? ? G MN . MN ? ? ? 1_555 M HOH . O ? ? B MN 101 B HOH 218 1_555 ? ? ? ? ? ? ? 2.231 ? ? hydrog1 hydrog ? ? A DA 1 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 1 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DA 1 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 1 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 2 N3 A ? ? 1_555 B DG 6 N1 ? ? A DC 2 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 B ? ? 1_555 B DG 6 N1 ? ? A DC 2 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 A ? ? 1_555 B DG 6 O6 ? ? A DC 2 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 N4 B ? ? 1_555 B DG 6 O6 ? ? A DC 2 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 2 O2 A ? ? 1_555 B DG 6 N2 ? ? A DC 2 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 2 O2 B ? ? 1_555 B DG 6 N2 ? ? A DC 2 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 3 B DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 3 B DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 3 B DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 N1 A ? ? 1_555 B 5CM 4 N3 A ? A DG 4 B 5CM 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 4 N2 A ? ? 1_555 B 5CM 4 O2 A ? A DG 4 B 5CM 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 4 O6 A ? ? 1_555 B 5CM 4 N4 A ? A DG 4 B 5CM 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 5 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 5 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 5 B DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 2 N3 A ? A DG 6 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 2 N3 B ? A DG 6 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 2 O2 A ? A DG 6 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 2 O2 B ? A DG 6 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 2 N4 A ? A DG 6 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 2 N4 B ? A DG 6 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 1 N1 ? ? A DT 7 B DA 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 1 N6 ? ? A DT 7 B DA 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? 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 N7 ? A DG 3 ? A DG 3 ? 1_555 MN ? F MN . ? A MN 102 ? 1_555 O ? L HOH . ? A HOH 207 ? 1_555 88.9 ? 2 N7 ? A DG 3 ? A DG 3 ? 1_555 MN ? F MN . ? A MN 102 ? 1_555 O ? L HOH . ? A HOH 216 ? 1_555 95.2 ? 3 O ? L HOH . ? A HOH 207 ? 1_555 MN ? F MN . ? A MN 102 ? 1_555 O ? L HOH . ? A HOH 216 ? 1_555 173.2 ? 4 N7 ? A DG 3 ? A DG 3 ? 1_555 MN ? F MN . ? A MN 102 ? 1_555 N7 ? B DG 3 ? B DG 3 ? 1_555 86.0 ? 5 O ? L HOH . ? A HOH 207 ? 1_555 MN ? F MN . ? A MN 102 ? 1_555 N7 ? B DG 3 ? B DG 3 ? 1_555 134.8 ? 6 O ? L HOH . ? A HOH 216 ? 1_555 MN ? F MN . ? A MN 102 ? 1_555 N7 ? B DG 3 ? B DG 3 ? 1_555 40.5 ? 7 N7 ? A DG 3 ? A DG 3 ? 1_555 MN ? F MN . ? A MN 102 ? 1_555 O ? M HOH . ? B HOH 205 ? 6_557 85.4 ? 8 O ? L HOH . ? A HOH 207 ? 1_555 MN ? F MN . ? A MN 102 ? 1_555 O ? M HOH . ? B HOH 205 ? 6_557 98.1 ? 9 O ? L HOH . ? A HOH 216 ? 1_555 MN ? F MN . ? A MN 102 ? 1_555 O ? M HOH . ? B HOH 205 ? 6_557 87.7 ? 10 N7 ? B DG 3 ? B DG 3 ? 1_555 MN ? F MN . ? A MN 102 ? 1_555 O ? M HOH . ? B HOH 205 ? 6_557 126.1 ? 11 N7 ? A DG 3 ? A DG 3 ? 1_555 MN ? F MN . ? A MN 102 ? 1_555 O ? M HOH . ? B HOH 213 ? 6_557 91.9 ? 12 O ? L HOH . ? A HOH 207 ? 1_555 MN ? F MN . ? A MN 102 ? 1_555 O ? M HOH . ? B HOH 213 ? 6_557 89.8 ? 13 O ? L HOH . ? A HOH 216 ? 1_555 MN ? F MN . ? A MN 102 ? 1_555 O ? M HOH . ? B HOH 213 ? 6_557 84.6 ? 14 N7 ? B DG 3 ? B DG 3 ? 1_555 MN ? F MN . ? A MN 102 ? 1_555 O ? M HOH . ? B HOH 213 ? 6_557 45.7 ? 15 O ? M HOH . ? B HOH 205 ? 6_557 MN ? F MN . ? A MN 102 ? 1_555 O ? M HOH . ? B HOH 213 ? 6_557 171.6 ? 16 N7 ? A DG 6 ? A DG 6 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? L HOH . ? A HOH 208 ? 1_555 92.7 ? 17 N7 ? A DG 6 ? A DG 6 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? L HOH . ? A HOH 212 ? 1_555 94.1 ? 18 O ? L HOH . ? A HOH 208 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? L HOH . ? A HOH 212 ? 1_555 118.2 ? 19 N7 ? A DG 6 ? A DG 6 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? L HOH . ? A HOH 215 ? 1_555 83.5 ? 20 O ? L HOH . ? A HOH 208 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? L HOH . ? A HOH 215 ? 1_555 62.2 ? 21 O ? L HOH . ? A HOH 212 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? L HOH . ? A HOH 215 ? 1_555 57.8 ? 22 N7 ? A DG 6 ? A DG 6 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? L HOH . ? A HOH 217 ? 1_555 93.2 ? 23 O ? L HOH . ? A HOH 208 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? L HOH . ? A HOH 217 ? 1_555 162.3 ? 24 O ? L HOH . ? A HOH 212 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? L HOH . ? A HOH 217 ? 1_555 77.9 ? 25 O ? L HOH . ? A HOH 215 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? L HOH . ? A HOH 217 ? 1_555 135.0 ? 26 N7 ? A DG 6 ? A DG 6 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? L HOH . ? A HOH 224 ? 1_555 143.5 ? 27 O ? L HOH . ? A HOH 208 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? L HOH . ? A HOH 224 ? 1_555 93.7 ? 28 O ? L HOH . ? A HOH 212 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? L HOH . ? A HOH 224 ? 1_555 114.0 ? 29 O ? L HOH . ? A HOH 215 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? L HOH . ? A HOH 224 ? 1_555 130.7 ? 30 O ? L HOH . ? A HOH 217 ? 1_555 MN ? E MN . ? A MN 101 ? 1_555 O ? L HOH . ? A HOH 224 ? 1_555 71.9 ? 31 N7 ? B DG 6 ? B DG 6 ? 1_555 MN ? G MN . ? B MN 101 ? 1_555 O ? M HOH . ? B HOH 212 ? 1_555 97.2 ? 32 N7 ? B DG 6 ? B DG 6 ? 1_555 MN ? G MN . ? B MN 101 ? 1_555 O ? M HOH . ? B HOH 215 ? 1_555 103.4 ? 33 O ? M HOH . ? B HOH 212 ? 1_555 MN ? G MN . ? B MN 101 ? 1_555 O ? M HOH . ? B HOH 215 ? 1_555 83.4 ? 34 N7 ? B DG 6 ? B DG 6 ? 1_555 MN ? G MN . ? B MN 101 ? 1_555 O ? M HOH . ? B HOH 218 ? 1_555 167.5 ? 35 O ? M HOH . ? B HOH 212 ? 1_555 MN ? G MN . ? B MN 101 ? 1_555 O ? M HOH . ? B HOH 218 ? 1_555 94.9 ? 36 O ? M HOH . ? B HOH 215 ? 1_555 MN ? G MN . ? B MN 101 ? 1_555 O ? M HOH . ? B HOH 218 ? 1_555 74.7 ? # 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 DG 3 ? ? P A DG 4 ? A 1.469 1.607 -0.138 0.012 Y 2 1 "O3'" A DG 3 ? ? P A DG 4 ? B 1.458 1.607 -0.149 0.012 Y 3 1 C D ALA 2 ? ? N D N2C 3 ? ? 1.494 1.336 0.158 0.023 Y 4 1 C D N2C 3 ? ? N D MVA 4 ? ? 1.506 1.336 0.170 0.023 Y 5 1 C D ALA 6 ? ? N D NCY 7 ? ? 1.477 1.336 0.141 0.023 Y 6 1 C D NCY 7 ? ? N D MVA 8 ? ? 1.501 1.336 0.165 0.023 Y 7 1 C E ALA 2 ? ? N E N2C 3 ? ? 1.479 1.336 0.143 0.023 Y 8 1 C E N2C 3 ? ? N E MVA 4 ? ? 1.498 1.336 0.162 0.023 Y 9 1 C E NCY 7 ? ? N E MVA 8 ? ? 1.492 1.336 0.156 0.023 Y # 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 "C3'" A DG 3 ? ? "O3'" A DG 3 ? ? P A DG 4 ? A 133.79 119.70 14.09 1.20 Y 2 1 "C3'" A DG 3 ? ? "O3'" A DG 3 ? ? P A DG 4 ? B 132.07 119.70 12.37 1.20 Y 3 1 C5 A DG 4 ? B C6 A DG 4 ? B O6 A DG 4 ? B 124.20 128.60 -4.40 0.60 N 4 1 C8 A DG 4 ? B N9 A DG 4 ? B "C1'" A DG 4 ? B 118.29 127.00 -8.71 1.30 N 5 1 C4 A DG 4 ? B N9 A DG 4 ? B "C1'" A DG 4 ? B 134.59 126.50 8.09 1.30 N 6 1 "O4'" B DA 1 ? ? "C1'" B DA 1 ? ? "C2'" B DA 1 ? ? 109.96 106.80 3.16 0.50 N 7 1 "O3'" B DC 2 ? A P B DG 3 ? ? OP2 B DG 3 ? ? 120.59 110.50 10.09 1.10 Y 8 1 "O3'" B DC 2 ? B P B DG 3 ? ? OP2 B DG 3 ? ? 122.83 110.50 12.33 1.10 Y # _pdbx_molecule_features.prd_id PRD_000491 _pdbx_molecule_features.name Echinomycin _pdbx_molecule_features.type 'Cyclic depsipeptide' _pdbx_molecule_features.class Antibiotic _pdbx_molecule_features.details ;ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5. ; # loop_ _pdbx_molecule.instance_id _pdbx_molecule.prd_id _pdbx_molecule.asym_id 1 PRD_000491 C 1 PRD_000491 H 1 PRD_000491 I 2 PRD_000491 D 2 PRD_000491 J 2 PRD_000491 K # loop_ _pdbx_refine_tls.id _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[1][1]_esd _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][2]_esd _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[1][3]_esd _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[2][2]_esd _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.T[2][3]_esd _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[3][3]_esd _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[1][1]_esd _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][2]_esd _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[1][3]_esd _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[2][2]_esd _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.L[2][3]_esd _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[3][3]_esd _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][1]_esd _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][2]_esd _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[1][3]_esd _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][1]_esd _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][2]_esd _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][3]_esd _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][1]_esd _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][2]_esd _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[3][3]_esd 1 'X-RAY DIFFRACTION' ? refined 39.5321 11.9059 47.9784 0.2863 ? 0.0048 ? 0.0131 ? 0.2565 ? -0.0105 ? 0.2958 ? 5.3321 ? 0.3096 ? -0.1349 ? 5.2939 ? 0.0856 ? 5.9995 ? 0.0376 ? 0.4163 ? -0.4250 ? 0.3952 ? -0.2958 ? -0.2908 ? 0.8966 ? 0.4022 ? 0.2415 ? 2 'X-RAY DIFFRACTION' ? refined 38.1949 14.0772 47.9596 0.2665 ? -0.0619 ? -0.0309 ? 0.3266 ? 0.0134 ? 0.2821 ? 3.0557 ? 0.0682 ? -0.3622 ? 2.8020 ? -0.3332 ? 2.4735 ? 0.3730 ? 0.5412 ? -0.1725 ? 0.5667 ? -0.2740 ? -0.0795 ? 0.5640 ? 0.3279 ? 0.0571 ? 3 'X-RAY DIFFRACTION' ? refined 36.0909 16.0748 59.9244 0.3074 ? -0.1752 ? -0.0516 ? 0.0193 ? -0.0365 ? 0.1325 ? 0.0441 ? -0.0198 ? 0.0106 ? 0.0619 ? 0.0068 ? 0.0047 ? -0.0097 ? 0.0121 ? -0.0112 ? 0.0097 ? -0.0078 ? 0.0597 ? 0.0107 ? -0.0113 ? -0.0059 ? 4 'X-RAY DIFFRACTION' ? refined 41.7445 18.5751 50.7064 0.2289 ? -0.1155 ? -0.0226 ? 0.3190 ? 0.0648 ? 0.1550 ? 0.1169 ? 0.0093 ? 0.1043 ? 0.0218 ? 0.0094 ? 0.1199 ? 0.0189 ? 0.0493 ? -0.0050 ? -0.0176 ? 0.0088 ? 0.0374 ? 0.0096 ? -0.0117 ? -0.0020 ? # loop_ _pdbx_refine_tls_group.id _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_PDB_ins_code _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_PDB_ins_code _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 1 'X-RAY DIFFRACTION' 1 ? ? ? ? ? ? ? ? ? ? ? ;chain 'D' ; 2 'X-RAY DIFFRACTION' 2 ? ? ? ? ? ? ? ? ? ? ? ;(chain 'A' and (resid 1 or resid 3 or resid 5 through 7)) or (chain 'B' and (resid 1 or resid 3 or resid 5 through 7)) ; 3 'X-RAY DIFFRACTION' 3 ? ? ? ? ? ? ? ? ? ? ? ;(chain 'B' and resid 2) ; 4 'X-RAY DIFFRACTION' 4 ? ? ? ? ? ? ? ? ? ? ? ;(chain 'B' and resid 4) ; # _pdbx_entry_details.entry_id 8XP8 _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ;THE ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. HERE, ECHINOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND TWO LIGANDS (HET) QUI. ; _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.has_protein_modification ? # 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 5CM N1 N N N 1 5CM C2 C N N 2 5CM N3 N N N 3 5CM C4 C N N 4 5CM C5 C N N 5 5CM C5A C N N 6 5CM C6 C N N 7 5CM O2 O N N 8 5CM N4 N N N 9 5CM "C1'" C N R 10 5CM "C2'" C N N 11 5CM "C3'" C N S 12 5CM "C4'" C N R 13 5CM "O4'" O N N 14 5CM "O3'" O N N 15 5CM "C5'" C N N 16 5CM "O5'" O N N 17 5CM P P N N 18 5CM OP1 O N N 19 5CM OP2 O N N 20 5CM OP3 O N N 21 5CM H5A1 H N N 22 5CM H5A2 H N N 23 5CM H5A3 H N N 24 5CM H6 H N N 25 5CM HN41 H N N 26 5CM HN42 H N N 27 5CM "H1'" H N N 28 5CM "H2'" H N N 29 5CM "H2''" H N N 30 5CM "H3'" H N N 31 5CM "H4'" H N N 32 5CM "HO3'" H N N 33 5CM "H5'" H N N 34 5CM "H5''" H N N 35 5CM HOP2 H N N 36 5CM HOP3 H N N 37 ALA N N N N 38 ALA CA C N S 39 ALA C C N N 40 ALA O O N N 41 ALA CB C N N 42 ALA OXT O N N 43 ALA H H N N 44 ALA H2 H N N 45 ALA HA H N N 46 ALA HB1 H N N 47 ALA HB2 H N N 48 ALA HB3 H N N 49 ALA HXT H N N 50 DA OP3 O N N 51 DA P P N N 52 DA OP1 O N N 53 DA OP2 O N N 54 DA "O5'" O N N 55 DA "C5'" C N N 56 DA "C4'" C N R 57 DA "O4'" O N N 58 DA "C3'" C N S 59 DA "O3'" O N N 60 DA "C2'" C N N 61 DA "C1'" C N R 62 DA N9 N Y N 63 DA C8 C Y N 64 DA N7 N Y N 65 DA C5 C Y N 66 DA C6 C Y N 67 DA N6 N N N 68 DA N1 N Y N 69 DA C2 C Y N 70 DA N3 N Y N 71 DA C4 C Y N 72 DA HOP3 H N N 73 DA HOP2 H N N 74 DA "H5'" H N N 75 DA "H5''" H N N 76 DA "H4'" H N N 77 DA "H3'" H N N 78 DA "HO3'" H N N 79 DA "H2'" H N N 80 DA "H2''" H N N 81 DA "H1'" H N N 82 DA H8 H N N 83 DA H61 H N N 84 DA H62 H N N 85 DA H2 H N N 86 DC OP3 O N N 87 DC P P N N 88 DC OP1 O N N 89 DC OP2 O N N 90 DC "O5'" O N N 91 DC "C5'" C N N 92 DC "C4'" C N R 93 DC "O4'" O N N 94 DC "C3'" C N S 95 DC "O3'" O N N 96 DC "C2'" C N N 97 DC "C1'" C N R 98 DC N1 N N N 99 DC C2 C N N 100 DC O2 O N N 101 DC N3 N N N 102 DC C4 C N N 103 DC N4 N N N 104 DC C5 C N N 105 DC C6 C N N 106 DC HOP3 H N N 107 DC HOP2 H N N 108 DC "H5'" H N N 109 DC "H5''" H N N 110 DC "H4'" H N N 111 DC "H3'" H N N 112 DC "HO3'" H N N 113 DC "H2'" H N N 114 DC "H2''" H N N 115 DC "H1'" H N N 116 DC H41 H N N 117 DC H42 H N N 118 DC H5 H N N 119 DC H6 H N N 120 DG OP3 O N N 121 DG P P N N 122 DG OP1 O N N 123 DG OP2 O N N 124 DG "O5'" O N N 125 DG "C5'" C N N 126 DG "C4'" C N R 127 DG "O4'" O N N 128 DG "C3'" C N S 129 DG "O3'" O N N 130 DG "C2'" C N N 131 DG "C1'" C N R 132 DG N9 N Y N 133 DG C8 C Y N 134 DG N7 N Y N 135 DG C5 C Y N 136 DG C6 C N N 137 DG O6 O N N 138 DG N1 N N N 139 DG C2 C N N 140 DG N2 N N N 141 DG N3 N N N 142 DG C4 C Y N 143 DG HOP3 H N N 144 DG HOP2 H N N 145 DG "H5'" H N N 146 DG "H5''" H N N 147 DG "H4'" H N N 148 DG "H3'" H N N 149 DG "HO3'" H N N 150 DG "H2'" H N N 151 DG "H2''" H N N 152 DG "H1'" H N N 153 DG H8 H N N 154 DG H1 H N N 155 DG H21 H N N 156 DG H22 H N N 157 DSN N N N N 158 DSN CA C N R 159 DSN C C N N 160 DSN O O N N 161 DSN OXT O N N 162 DSN CB C N N 163 DSN OG O N N 164 DSN H H N N 165 DSN H2 H N N 166 DSN HA H N N 167 DSN HXT H N N 168 DSN HB2 H N N 169 DSN HB3 H N N 170 DSN HG H N N 171 DT OP3 O N N 172 DT P P N N 173 DT OP1 O N N 174 DT OP2 O N N 175 DT "O5'" O N N 176 DT "C5'" C N N 177 DT "C4'" C N R 178 DT "O4'" O N N 179 DT "C3'" C N S 180 DT "O3'" O N N 181 DT "C2'" C N N 182 DT "C1'" C N R 183 DT N1 N N N 184 DT C2 C N N 185 DT O2 O N N 186 DT N3 N N N 187 DT C4 C N N 188 DT O4 O N N 189 DT C5 C N N 190 DT C7 C N N 191 DT C6 C N N 192 DT HOP3 H N N 193 DT HOP2 H N N 194 DT "H5'" H N N 195 DT "H5''" H N N 196 DT "H4'" H N N 197 DT "H3'" H N N 198 DT "HO3'" H N N 199 DT "H2'" H N N 200 DT "H2''" H N N 201 DT "H1'" H N N 202 DT H3 H N N 203 DT H71 H N N 204 DT H72 H N N 205 DT H73 H N N 206 DT H6 H N N 207 HOH O O N N 208 HOH H1 H N N 209 HOH H2 H N N 210 MN MN MN N N 211 MVA N N N N 212 MVA CN C N N 213 MVA CA C N S 214 MVA CB C N N 215 MVA CG1 C N N 216 MVA CG2 C N N 217 MVA C C N N 218 MVA O O N N 219 MVA OXT O N N 220 MVA H H N N 221 MVA HN1 H N N 222 MVA HN2 H N N 223 MVA HN3 H N N 224 MVA HA H N N 225 MVA HB H N N 226 MVA HG11 H N N 227 MVA HG12 H N N 228 MVA HG13 H N N 229 MVA HG21 H N N 230 MVA HG22 H N N 231 MVA HG23 H N N 232 MVA HXT H N N 233 N2C N N N N 234 N2C CA C N R 235 N2C CB C N N 236 N2C SG S N N 237 N2C CD C N N 238 N2C CN C N N 239 N2C C C N N 240 N2C O O N N 241 N2C OXT O N N 242 N2C H H N N 243 N2C HA H N N 244 N2C HB2 H N N 245 N2C HB3 H N N 246 N2C HD1 H N N 247 N2C HD2 H N N 248 N2C HD3 H N N 249 N2C HN1 H N N 250 N2C HN2 H N N 251 N2C HN3 H N N 252 N2C HXT H N N 253 NCY N N N N 254 NCY CA C N R 255 NCY CB C N N 256 NCY SG S N N 257 NCY CN C N N 258 NCY C C N N 259 NCY O O N N 260 NCY OXT O N N 261 NCY H H N N 262 NCY HA H N N 263 NCY HB2 H N N 264 NCY HB3 H N N 265 NCY HG H N N 266 NCY HCN1 H N N 267 NCY HCN2 H N N 268 NCY HCN3 H N N 269 NCY HXT H N N 270 QUI N1 N Y N 271 QUI C2 C Y N 272 QUI C3 C Y N 273 QUI N4 N Y N 274 QUI C5 C Y N 275 QUI C6 C Y N 276 QUI C7 C Y N 277 QUI C8 C Y N 278 QUI C9 C Y N 279 QUI C10 C Y N 280 QUI C C N N 281 QUI O1 O N N 282 QUI O2 O N N 283 QUI H3 H N N 284 QUI H5 H N N 285 QUI H6 H N N 286 QUI H7 H N N 287 QUI H8 H N N 288 QUI HO2 H N N 289 # 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 5CM N1 C2 sing N N 1 5CM N1 C6 sing N N 2 5CM N1 "C1'" sing N N 3 5CM C2 N3 sing N N 4 5CM C2 O2 doub N N 5 5CM N3 C4 doub N N 6 5CM C4 C5 sing N N 7 5CM C4 N4 sing N N 8 5CM C5 C5A sing N N 9 5CM C5 C6 doub N N 10 5CM C5A H5A1 sing N N 11 5CM C5A H5A2 sing N N 12 5CM C5A H5A3 sing N N 13 5CM C6 H6 sing N N 14 5CM N4 HN41 sing N N 15 5CM N4 HN42 sing N N 16 5CM "C1'" "C2'" sing N N 17 5CM "C1'" "O4'" sing N N 18 5CM "C1'" "H1'" sing N N 19 5CM "C2'" "C3'" sing N N 20 5CM "C2'" "H2'" sing N N 21 5CM "C2'" "H2''" sing N N 22 5CM "C3'" "C4'" sing N N 23 5CM "C3'" "O3'" sing N N 24 5CM "C3'" "H3'" sing N N 25 5CM "C4'" "O4'" sing N N 26 5CM "C4'" "C5'" sing N N 27 5CM "C4'" "H4'" sing N N 28 5CM "O3'" "HO3'" sing N N 29 5CM "C5'" "O5'" sing N N 30 5CM "C5'" "H5'" sing N N 31 5CM "C5'" "H5''" sing N N 32 5CM "O5'" P sing N N 33 5CM P OP1 doub N N 34 5CM P OP2 sing N N 35 5CM P OP3 sing N N 36 5CM OP2 HOP2 sing N N 37 5CM OP3 HOP3 sing N N 38 ALA N CA sing N N 39 ALA N H sing N N 40 ALA N H2 sing N N 41 ALA CA C sing N N 42 ALA CA CB sing N N 43 ALA CA HA sing N N 44 ALA C O doub N N 45 ALA C OXT sing N N 46 ALA CB HB1 sing N N 47 ALA CB HB2 sing N N 48 ALA CB HB3 sing N N 49 ALA OXT HXT sing N N 50 DA OP3 P sing N N 51 DA OP3 HOP3 sing N N 52 DA P OP1 doub N N 53 DA P OP2 sing N N 54 DA P "O5'" sing N N 55 DA OP2 HOP2 sing N N 56 DA "O5'" "C5'" sing N N 57 DA "C5'" "C4'" sing N N 58 DA "C5'" "H5'" sing N N 59 DA "C5'" "H5''" sing N N 60 DA "C4'" "O4'" sing N N 61 DA "C4'" "C3'" sing N N 62 DA "C4'" "H4'" sing N N 63 DA "O4'" "C1'" sing N N 64 DA "C3'" "O3'" sing N N 65 DA "C3'" "C2'" sing N N 66 DA "C3'" "H3'" sing N N 67 DA "O3'" "HO3'" sing N N 68 DA "C2'" "C1'" sing N N 69 DA "C2'" "H2'" sing N N 70 DA "C2'" "H2''" sing N N 71 DA "C1'" N9 sing N N 72 DA "C1'" "H1'" sing N N 73 DA N9 C8 sing Y N 74 DA N9 C4 sing Y N 75 DA C8 N7 doub Y N 76 DA C8 H8 sing N N 77 DA N7 C5 sing Y N 78 DA C5 C6 sing Y N 79 DA C5 C4 doub Y N 80 DA C6 N6 sing N N 81 DA C6 N1 doub Y N 82 DA N6 H61 sing N N 83 DA N6 H62 sing N N 84 DA N1 C2 sing Y N 85 DA C2 N3 doub Y N 86 DA C2 H2 sing N N 87 DA N3 C4 sing Y N 88 DC OP3 P sing N N 89 DC OP3 HOP3 sing N N 90 DC P OP1 doub N N 91 DC P OP2 sing N N 92 DC P "O5'" sing N N 93 DC OP2 HOP2 sing N N 94 DC "O5'" "C5'" sing N N 95 DC "C5'" "C4'" sing N N 96 DC "C5'" "H5'" sing N N 97 DC "C5'" "H5''" sing N N 98 DC "C4'" "O4'" sing N N 99 DC "C4'" "C3'" sing N N 100 DC "C4'" "H4'" sing N N 101 DC "O4'" "C1'" sing N N 102 DC "C3'" "O3'" sing N N 103 DC "C3'" "C2'" sing N N 104 DC "C3'" "H3'" sing N N 105 DC "O3'" "HO3'" sing N N 106 DC "C2'" "C1'" sing N N 107 DC "C2'" "H2'" sing N N 108 DC "C2'" "H2''" sing N N 109 DC "C1'" N1 sing N N 110 DC "C1'" "H1'" sing N N 111 DC N1 C2 sing N N 112 DC N1 C6 sing N N 113 DC C2 O2 doub N N 114 DC C2 N3 sing N N 115 DC N3 C4 doub N N 116 DC C4 N4 sing N N 117 DC C4 C5 sing N N 118 DC N4 H41 sing N N 119 DC N4 H42 sing N N 120 DC C5 C6 doub N N 121 DC C5 H5 sing N N 122 DC C6 H6 sing N N 123 DG OP3 P sing N N 124 DG OP3 HOP3 sing N N 125 DG P OP1 doub N N 126 DG P OP2 sing N N 127 DG P "O5'" sing N N 128 DG OP2 HOP2 sing N N 129 DG "O5'" "C5'" sing N N 130 DG "C5'" "C4'" sing N N 131 DG "C5'" "H5'" sing N N 132 DG "C5'" "H5''" sing N N 133 DG "C4'" "O4'" sing N N 134 DG "C4'" "C3'" sing N N 135 DG "C4'" "H4'" sing N N 136 DG "O4'" "C1'" sing N N 137 DG "C3'" "O3'" sing N N 138 DG "C3'" "C2'" sing N N 139 DG "C3'" "H3'" sing N N 140 DG "O3'" "HO3'" sing N N 141 DG "C2'" "C1'" sing N N 142 DG "C2'" "H2'" sing N N 143 DG "C2'" "H2''" sing N N 144 DG "C1'" N9 sing N N 145 DG "C1'" "H1'" sing N N 146 DG N9 C8 sing Y N 147 DG N9 C4 sing Y N 148 DG C8 N7 doub Y N 149 DG C8 H8 sing N N 150 DG N7 C5 sing Y N 151 DG C5 C6 sing N N 152 DG C5 C4 doub Y N 153 DG C6 O6 doub N N 154 DG C6 N1 sing N N 155 DG N1 C2 sing N N 156 DG N1 H1 sing N N 157 DG C2 N2 sing N N 158 DG C2 N3 doub N N 159 DG N2 H21 sing N N 160 DG N2 H22 sing N N 161 DG N3 C4 sing N N 162 DSN N CA sing N N 163 DSN N H sing N N 164 DSN N H2 sing N N 165 DSN CA C sing N N 166 DSN CA CB sing N N 167 DSN CA HA sing N N 168 DSN C O doub N N 169 DSN C OXT sing N N 170 DSN OXT HXT sing N N 171 DSN CB OG sing N N 172 DSN CB HB2 sing N N 173 DSN CB HB3 sing N N 174 DSN OG HG sing N N 175 DT OP3 P sing N N 176 DT OP3 HOP3 sing N N 177 DT P OP1 doub N N 178 DT P OP2 sing N N 179 DT P "O5'" sing N N 180 DT OP2 HOP2 sing N N 181 DT "O5'" "C5'" sing N N 182 DT "C5'" "C4'" sing N N 183 DT "C5'" "H5'" sing N N 184 DT "C5'" "H5''" sing N N 185 DT "C4'" "O4'" sing N N 186 DT "C4'" "C3'" sing N N 187 DT "C4'" "H4'" sing N N 188 DT "O4'" "C1'" sing N N 189 DT "C3'" "O3'" sing N N 190 DT "C3'" "C2'" sing N N 191 DT "C3'" "H3'" sing N N 192 DT "O3'" "HO3'" sing N N 193 DT "C2'" "C1'" sing N N 194 DT "C2'" "H2'" sing N N 195 DT "C2'" "H2''" sing N N 196 DT "C1'" N1 sing N N 197 DT "C1'" "H1'" sing N N 198 DT N1 C2 sing N N 199 DT N1 C6 sing N N 200 DT C2 O2 doub N N 201 DT C2 N3 sing N N 202 DT N3 C4 sing N N 203 DT N3 H3 sing N N 204 DT C4 O4 doub N N 205 DT C4 C5 sing N N 206 DT C5 C7 sing N N 207 DT C5 C6 doub N N 208 DT C7 H71 sing N N 209 DT C7 H72 sing N N 210 DT C7 H73 sing N N 211 DT C6 H6 sing N N 212 HOH O H1 sing N N 213 HOH O H2 sing N N 214 MVA N CN sing N N 215 MVA N CA sing N N 216 MVA N H sing N N 217 MVA CN HN1 sing N N 218 MVA CN HN2 sing N N 219 MVA CN HN3 sing N N 220 MVA CA CB sing N N 221 MVA CA C sing N N 222 MVA CA HA sing N N 223 MVA CB CG1 sing N N 224 MVA CB CG2 sing N N 225 MVA CB HB sing N N 226 MVA CG1 HG11 sing N N 227 MVA CG1 HG12 sing N N 228 MVA CG1 HG13 sing N N 229 MVA CG2 HG21 sing N N 230 MVA CG2 HG22 sing N N 231 MVA CG2 HG23 sing N N 232 MVA C O doub N N 233 MVA C OXT sing N N 234 MVA OXT HXT sing N N 235 N2C N CA sing N N 236 N2C N CN sing N N 237 N2C N H sing N N 238 N2C CA CB sing N N 239 N2C CA C sing N N 240 N2C CA HA sing N N 241 N2C CB SG sing N N 242 N2C CB HB2 sing N N 243 N2C CB HB3 sing N N 244 N2C SG CD sing N N 245 N2C CD HD1 sing N N 246 N2C CD HD2 sing N N 247 N2C CD HD3 sing N N 248 N2C CN HN1 sing N N 249 N2C CN HN2 sing N N 250 N2C CN HN3 sing N N 251 N2C C O doub N N 252 N2C C OXT sing N N 253 N2C OXT HXT sing N N 254 NCY N CA sing N N 255 NCY N CN sing N N 256 NCY N H sing N N 257 NCY CA CB sing N N 258 NCY CA C sing N N 259 NCY CA HA sing N N 260 NCY CB SG sing N N 261 NCY CB HB2 sing N N 262 NCY CB HB3 sing N N 263 NCY SG HG sing N N 264 NCY CN HCN1 sing N N 265 NCY CN HCN2 sing N N 266 NCY CN HCN3 sing N N 267 NCY C O doub N N 268 NCY C OXT sing N N 269 NCY OXT HXT sing N N 270 QUI N1 C2 doub Y N 271 QUI N1 C9 sing Y N 272 QUI C2 C3 sing Y N 273 QUI C2 C sing N N 274 QUI C3 N4 doub Y N 275 QUI C3 H3 sing N N 276 QUI N4 C10 sing Y N 277 QUI C5 C6 doub Y N 278 QUI C5 C10 sing Y N 279 QUI C5 H5 sing N N 280 QUI C6 C7 sing Y N 281 QUI C6 H6 sing N N 282 QUI C7 C8 doub Y N 283 QUI C7 H7 sing N N 284 QUI C8 C9 sing Y N 285 QUI C8 H8 sing N N 286 QUI C9 C10 doub Y N 287 QUI C O1 doub N N 288 QUI C O2 sing N N 289 QUI O2 HO2 sing N N 290 # _ndb_struct_conf_na.entry_id 8XP8 _ndb_struct_conf_na.feature '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 DA 1 1_555 B DT 7 1_555 0.394 -0.199 0.127 1.359 -0.643 2.585 1 A_DA1:DT7_B A 1 ? B 7 ? 20 1 1 A DC 2 1_555 B DG 6 1_555 0.320 -0.211 0.132 -18.320 6.092 -1.032 2 A_DC2:DG6_B A 2 ? B 6 ? 19 1 1 A DG 3 1_555 B DC 5 1_555 -0.309 -0.169 0.070 19.823 6.493 -2.419 3 A_DG3:DC5_B A 3 ? B 5 ? 19 1 1 A DG 4 1_555 B 5CM 4 1_555 0.317 -0.420 0.507 9.560 2.472 -2.774 4 A_DG4:5CM4_B A 4 ? B 4 ? 19 1 1 A DC 5 1_555 B DG 3 1_555 0.332 -0.148 0.067 -18.978 5.172 -2.715 5 A_DC5:DG3_B A 5 ? B 3 ? 19 1 1 A DG 6 1_555 B DC 2 1_555 -0.792 -0.155 0.001 18.200 0.512 0.722 6 A_DG6:DC2_B A 6 ? B 2 ? 19 1 1 A DT 7 1_555 B DA 1 1_555 -0.203 -0.167 0.137 -2.761 4.263 3.060 7 A_DT7:DA1_B A 7 ? B 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 A DA 1 1_555 B DT 7 1_555 A DC 2 1_555 B DG 6 1_555 0.416 0.775 6.822 9.715 2.009 15.183 0.013 10.507 6.030 6.745 -32.614 18.121 1 AA_DA1DC2:DG6DT7_BB A 1 ? B 7 ? A 2 ? B 6 ? 1 A DC 2 1_555 B DG 6 1_555 A DG 3 1_555 B DC 5 1_555 -0.055 2.647 2.605 0.705 -1.989 10.794 16.034 1.077 2.076 -10.441 -3.704 10.998 2 AA_DC2DG3:DC5DG6_BB A 2 ? B 6 ? A 3 ? B 5 ? 1 A DG 3 1_555 B DC 5 1_555 A DG 4 1_555 B 5CM 4 1_555 -0.392 0.505 6.853 -13.386 -6.856 17.021 6.547 -9.280 5.237 -19.024 37.142 22.677 3 AA_DG3DG4:5CM4DC5_BB A 3 ? B 5 ? A 4 ? B 4 ? 1 A DG 4 1_555 B 5CM 4 1_555 A DC 5 1_555 B DG 3 1_555 0.738 1.054 7.207 14.380 -1.718 14.592 4.698 12.500 5.562 -5.341 -44.696 20.532 4 AA_DG4DC5:DG35CM4_BB A 4 ? B 4 ? A 5 ? B 3 ? 1 A DC 5 1_555 B DG 3 1_555 A DG 6 1_555 B DC 2 1_555 0.198 2.663 2.712 -0.575 -1.086 10.193 16.398 -1.910 2.401 -6.086 3.223 10.266 5 AA_DC5DG6:DC2DG3_BB A 5 ? B 3 ? A 6 ? B 2 ? 1 A DG 6 1_555 B DC 2 1_555 A DT 7 1_555 B DA 1 1_555 -0.632 0.872 6.816 -10.616 -0.868 16.508 3.458 -9.145 6.042 -2.688 32.887 19.626 6 AA_DG6DT7:DA1DC2_BB A 6 ? B 2 ? A 7 ? B 1 ? # _pdbx_audit_support.funding_organization 'Ministry of Science and Technology (MoST, Taiwan)' _pdbx_audit_support.country Taiwan _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 5YTZ _pdbx_initial_refinement_model.details ? # _atom_sites.entry_id 8XP8 _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.021585 _atom_sites.fract_transf_matrix[1][2] 0.012462 _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] 0.024924 _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] 0.020853 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C MN N O P S # loop_