data_1PFE # _entry.id 1PFE # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1PFE pdb_00001pfe 10.2210/pdb1pfe/pdb NDB DD0057 ? ? RCSB RCSB019291 ? ? WWPDB D_1000019291 ? ? # 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 2004-06-08 2 'Structure model' 1 1 2011-06-14 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2011-07-27 5 'Structure model' 1 4 2012-12-12 6 'Structure model' 1 5 2024-04-03 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Atomic model' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Non-polymer description' 7 4 'Structure model' 'Structure summary' 8 5 'Structure model' Other 9 6 'Structure model' Advisory 10 6 'Structure model' 'Data collection' 11 6 'Structure model' 'Database references' 12 6 'Structure model' 'Derived calculations' 13 6 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 6 'Structure model' chem_comp_atom 2 6 'Structure model' chem_comp_bond 3 6 'Structure model' database_2 4 6 'Structure model' diffrn_source 5 6 'Structure model' pdbx_initial_refinement_model 6 6 'Structure model' pdbx_validate_polymer_linkage 7 6 'Structure model' struct_conn 8 6 'Structure model' struct_ref_seq_dif 9 6 '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 6 'Structure model' '_database_2.pdbx_DOI' 2 6 'Structure model' '_database_2.pdbx_database_accession' 3 6 'Structure model' '_diffrn_source.pdbx_synchrotron_site' 4 6 'Structure model' '_struct_conn.pdbx_dist_value' 5 6 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 6 6 'Structure model' '_struct_conn.pdbx_ptnr1_label_alt_id' 7 6 'Structure model' '_struct_conn.pdbx_ptnr2_label_alt_id' 8 6 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 9 6 'Structure model' '_struct_conn.ptnr1_label_atom_id' 10 6 'Structure model' '_struct_conn.ptnr1_label_comp_id' 11 6 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 12 6 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 13 6 'Structure model' '_struct_conn.ptnr2_label_asym_id' 14 6 'Structure model' '_struct_conn.ptnr2_label_atom_id' 15 6 'Structure model' '_struct_conn.ptnr2_label_comp_id' 16 6 'Structure model' '_struct_conn.ptnr2_label_seq_id' 17 6 'Structure model' '_struct_ref_seq_dif.details' 18 6 'Structure model' '_struct_site.pdbx_auth_asym_id' 19 6 'Structure model' '_struct_site.pdbx_auth_comp_id' 20 6 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1PFE _pdbx_database_status.recvd_initial_deposition_date 2003-05-26 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 185D unspecified 'SOLUTION STRUCTURE OF D(GACGTC) COMPLEXED WITH TRIOSTIN A' PDB 193D unspecified 'SOLUTION STRUCTURE OF D(ACACGTGT) COMPLEXED WITH QUINOMYCIN UK-6305' PDB 1VS2 unspecified 'CRYSTAL STRUCTURE OF D(GCGTACGC) COMPLEXED WITH TRIOSIN A' PDB 1XVK unspecified 'CRYSTAL STRUCTURE OF D(GCGTACGC) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P632' PDB 1XVN unspecified 'CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P632' PDB 1XVR unspecified 'CRYSTAL STRUCTURE OF D(CGTACG) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP C21' PDB 2ADW unspecified 'CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P42212' PDB 2DA8 unspecified 'SOLUTION STRUCTURE OF D(GATATC) COMPLEXED WITH A MODIFIED TRIOSTIN A AT POSITIONS 4 AND 8' PDB 3GO3 unspecified 'CRYSTAL STRUCTURE OF D(ACGTACGT) COMPLEXED WITH ECHINOMYCIN - SPACE GROUP P41212' # _audit_author.name 'Cuesta-Seijo, J.A.' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title 'Structures of Complexes between Echinomycin and Duplex DNA.' _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume 61 _citation.page_first 442 _citation.page_last ? _citation.year 2005 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15805599 _citation.pdbx_database_id_DOI 10.1107/S090744490500137X # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Cuesta-Seijo, J.A.' 1 ? primary 'Sheldrick, G.M.' 2 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-D(*GP*CP*GP*TP*AP*CP*GP*C)-3'" 2427.605 1 ? ? ? ? 2 polymer nat ECHINOMYCIN 809.008 1 ? ? ? ? 3 non-polymer syn 'CHLORIDE ION' 35.453 1 ? ? ? ? 4 non-polymer syn 2-CARBOXYQUINOXALINE 174.156 2 ? ? ? ? 5 water nat water 18.015 80 ? ? ? ? # _entity_name_com.entity_id 2 _entity_name_com.name 'QUINOMYCIN A' # 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 '(DG)(DC)(DG)(DT)(DA)(DC)(DG)(DC)' GCGTACGC A ? 2 'polypeptide(L)' no yes '(DSN)A(N2C)(MVA)(DSN)A(NCY)(MVA)' SAXVSAXV B ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'CHLORIDE ION' CL 4 2-CARBOXYQUINOXALINE QUI 5 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 DC n 1 3 DG n 1 4 DT n 1 5 DA n 1 6 DC n 1 7 DG n 1 8 DC n 2 1 DSN n 2 2 ALA n 2 3 N2C y 2 3 NCY y 2 4 MVA n 2 5 DSN n 2 6 ALA n 2 7 NCY y 2 7 N2C y 2 8 MVA n # _entity_src_nat.entity_id 2 _entity_src_nat.pdbx_src_id 1 _entity_src_nat.pdbx_alt_source_flag sample _entity_src_nat.pdbx_beg_seq_num ? _entity_src_nat.pdbx_end_seq_num ? _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_ _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 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 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 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 DG 1 1 1 DG DG 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 DT 4 4 4 DT DT A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DC 6 6 6 DC DC A . n A 1 7 DG 7 7 7 DG DG A . n A 1 8 DC 8 8 8 DC DC A . n B 2 1 DSN 1 1 1 DSN DSN B . n B 2 2 ALA 2 2 2 ALA ALA B . n B 2 3 N2C 3 3 3 N2C N2C B . y B 2 3 NCY 3 3 3 NCY NCY B . y B 2 4 MVA 4 4 4 MVA MVA B . n B 2 5 DSN 5 5 5 DSN DSN B . n B 2 6 ALA 6 6 6 ALA ALA B . n B 2 7 NCY 7 7 7 NCY NCY B . y B 2 7 N2C 7 7 7 N2C N2C B . y B 2 8 MVA 8 8 8 MVA MVA B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 3 CL 1 20 20 CL CL A . D 4 QUI 1 0 0 QUI QUI B . E 4 QUI 1 9 9 QUI QUI B . F 5 HOH 1 2001 2001 HOH HOH A . F 5 HOH 2 2002 2002 HOH HOH A . F 5 HOH 3 2003 2003 HOH HOH A . F 5 HOH 4 2004 2004 HOH HOH A . F 5 HOH 5 2005 2005 HOH HOH A . F 5 HOH 6 2006 2006 HOH HOH A . F 5 HOH 7 2007 2007 HOH HOH A . F 5 HOH 8 2008 2008 HOH HOH A . F 5 HOH 9 2009 2009 HOH HOH A . F 5 HOH 10 2010 2010 HOH HOH A . F 5 HOH 11 2011 2011 HOH HOH A . F 5 HOH 12 2012 2012 HOH HOH A . F 5 HOH 13 2013 2013 HOH HOH A . F 5 HOH 14 2014 2014 HOH HOH A . F 5 HOH 15 2015 2015 HOH HOH A . F 5 HOH 16 2016 2016 HOH HOH A . F 5 HOH 17 2017 2017 HOH HOH A . F 5 HOH 18 2018 2018 HOH HOH A . F 5 HOH 19 2019 2019 HOH HOH A . F 5 HOH 20 2020 2020 HOH HOH A . F 5 HOH 21 2021 2021 HOH HOH A . F 5 HOH 22 2022 2022 HOH HOH A . F 5 HOH 23 2023 2023 HOH HOH A . F 5 HOH 24 2024 2024 HOH HOH A . F 5 HOH 25 2025 2025 HOH HOH A . F 5 HOH 26 2026 2026 HOH HOH A . F 5 HOH 27 2027 2027 HOH HOH A . F 5 HOH 28 2028 2028 HOH HOH A . F 5 HOH 29 2029 2029 HOH HOH A . F 5 HOH 30 2030 2030 HOH HOH A . F 5 HOH 31 2031 2031 HOH HOH A . F 5 HOH 32 2032 2032 HOH HOH A . F 5 HOH 33 2033 2033 HOH HOH A . F 5 HOH 34 2034 2034 HOH HOH A . F 5 HOH 35 2035 2035 HOH HOH A . F 5 HOH 36 2036 2036 HOH HOH A . F 5 HOH 37 2037 2037 HOH HOH A . F 5 HOH 38 2038 2038 HOH HOH A . F 5 HOH 39 2039 2039 HOH HOH A . F 5 HOH 40 2040 2040 HOH HOH A . F 5 HOH 41 2041 2041 HOH HOH A . F 5 HOH 42 2042 2042 HOH HOH A . F 5 HOH 43 2043 2043 HOH HOH A . F 5 HOH 44 2044 2044 HOH HOH A . F 5 HOH 45 2045 2045 HOH HOH A . F 5 HOH 46 2046 2046 HOH HOH A . F 5 HOH 47 2047 2047 HOH HOH A . F 5 HOH 48 2048 2048 HOH HOH A . F 5 HOH 49 2049 2049 HOH HOH A . F 5 HOH 50 2050 2050 HOH HOH A . F 5 HOH 51 2051 2051 HOH HOH A . F 5 HOH 52 2052 2052 HOH HOH A . F 5 HOH 53 2053 2053 HOH HOH A . F 5 HOH 54 2054 2054 HOH HOH A . F 5 HOH 55 2055 2055 HOH HOH A . F 5 HOH 56 2056 2056 HOH HOH A . F 5 HOH 57 2057 2057 HOH HOH A . F 5 HOH 58 2058 2058 HOH HOH A . F 5 HOH 59 2059 2059 HOH HOH A . F 5 HOH 60 2060 2060 HOH HOH A . F 5 HOH 61 2061 2061 HOH HOH A . F 5 HOH 62 2062 2062 HOH HOH A . F 5 HOH 63 2063 2063 HOH HOH A . F 5 HOH 64 2064 2064 HOH HOH A . F 5 HOH 65 2065 2065 HOH HOH A . F 5 HOH 66 2066 2066 HOH HOH A . F 5 HOH 67 2067 2067 HOH HOH A . F 5 HOH 68 2068 2068 HOH HOH A . F 5 HOH 69 2069 2069 HOH HOH A . F 5 HOH 70 2070 2070 HOH HOH A . G 5 HOH 1 2001 2001 HOH HOH B . G 5 HOH 2 2002 2002 HOH HOH B . G 5 HOH 3 2003 2003 HOH HOH B . G 5 HOH 4 2004 2004 HOH HOH B . G 5 HOH 5 2005 2005 HOH HOH B . G 5 HOH 6 2006 2006 HOH HOH B . G 5 HOH 7 2007 2007 HOH HOH B . G 5 HOH 8 2008 2008 HOH HOH B . G 5 HOH 9 2009 2009 HOH HOH B . G 5 HOH 10 2010 2010 HOH HOH B . # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 B N2C 3 ? CD ? B N2C 3 CD 2 1 Y 1 B NCY 7 ? CD ? B NCY 7 CD # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal EPMR phasing . ? 1 SHELXL-97 refinement . ? 2 DENZO 'data reduction' . ? 3 SCALEPACK 'data scaling' . ? 4 # _cell.entry_id 1PFE _cell.length_a 39.374 _cell.length_b 39.374 _cell.length_c 79.734 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _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 1PFE _symmetry.space_group_name_H-M 'P 63 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1PFE _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.51 _exptl_crystal.density_percent_sol 64.98 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 4.5 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details 'LI2SO4, MGCL2, METHANOL, NAAC, SPERMINE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K' # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 Li2SO4 ? ? ? 1 2 1 MgCl2 ? ? ? 1 3 1 Methanol ? ? ? 1 4 1 NaAc ? ? ? 1 5 1 Spermine ? ? ? 1 6 1 H2O ? ? ? 1 7 2 MgCl2 ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2002-11-19 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'TRIANGULAR MONOCHROMATOR' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.8162 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'EMBL/DESY, HAMBURG BEAMLINE X11' _diffrn_source.pdbx_synchrotron_site 'EMBL/DESY, HAMBURG' _diffrn_source.pdbx_synchrotron_beamline X11 _diffrn_source.pdbx_wavelength 0.8162 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 1PFE _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 21.000 _reflns.d_resolution_high 1.100 _reflns.number_obs 15164 _reflns.number_all ? _reflns.percent_possible_obs 97.2 _reflns.pdbx_Rmerge_I_obs 0.04900 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 30.0100 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 14.910 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.10 _reflns_shell.d_res_low 1.20 _reflns_shell.percent_possible_all 95.7 _reflns_shell.Rmerge_I_obs 0.24200 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 11.480 _reflns_shell.pdbx_redundancy 13.05 _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 ? # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 1PFE _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all 15164 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 21.00 _refine.ls_d_res_high 1.10 _refine.ls_percent_reflns_obs 97.2 _refine.ls_R_factor_obs 0.146 _refine.ls_R_factor_all 0.146 _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free 0.168 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 3.000 _refine.ls_number_reflns_R_free 478 _refine.ls_number_parameters 2979 _refine.ls_number_restraints 2074 _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method 'FREE R' _refine.details ;THE SKELETON OF ECHINOMYCIN IS NEARLY SYMMETRIC (NOT MODELLED TO DO SO), THE BRIDGE IS NOT. BOTH POSSIBLE ORIENTATIONS OF BINDING WERE OBSERVED, BUT SKELETON POSITIONS NEARLY OVERLAP, SO ONLY THE BRIDGE WAS MODELLED AS DISORDERED/MICROHETEROGENEITY. ; _refine.pdbx_starting_model 'TROSTIN A - (GCGTACGC)2 COMPLEX' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'STANDARD SHELX FOR THE DNA, ENGH & HUBER FOR THE STANDARD PROTEIN PARTS OF ECHINOMYCIN, BUILT FROM THE CSD FOR THE REST' _refine.pdbx_stereochem_target_val_spec_case 'TARGETS FOR ECHINOMYCIN BUILT FROM THE CSD' _refine.pdbx_R_Free_selection_details 'THIN SHELLS' _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.ls_redundancy_reflns_obs ? _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_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_analyze.entry_id 1PFE _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues 7 _refine_analyze.occupancy_sum_hydrogen 149.00 _refine_analyze.occupancy_sum_non_hydrogen 303.00 # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 66 _refine_hist.pdbx_number_atoms_nucleic_acid 161 _refine_hist.pdbx_number_atoms_ligand 25 _refine_hist.number_atoms_solvent 80 _refine_hist.number_atoms_total 332 _refine_hist.d_res_high 1.10 _refine_hist.d_res_low 21.00 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function s_bond_d 0.022 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.036 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist ? ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes 0.172 ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol 0.068 ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol 0.059 ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr 0.041 ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 1.1 _refine_ls_shell.d_res_low 1.2 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work ? _refine_ls_shell.percent_reflns_obs 95.7 _refine_ls_shell.R_factor_R_free ? _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.R_factor_all ? # _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.entry_id 1PFE _pdbx_refine.R_factor_all_no_cutoff 0.146 _pdbx_refine.R_factor_obs_no_cutoff 0.146 _pdbx_refine.free_R_factor_no_cutoff 0.168 _pdbx_refine.free_R_error_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 3.000 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 478 _pdbx_refine.R_factor_all_4sig_cutoff ? _pdbx_refine.R_factor_obs_4sig_cutoff 0.138 _pdbx_refine.free_R_factor_4sig_cutoff 0.160 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff ? _pdbx_refine.number_reflns_obs_4sig_cutoff ? # _database_PDB_matrix.entry_id 1PFE _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 1PFE _struct.title 'Echinomycin-(gcgtacgc)2 complex' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1PFE _struct_keywords.pdbx_keywords DNA/ANTIBIOTIC _struct_keywords.text 'BISINTERCALATOR, HOOGSTEEN BASEPAIR, DEPSIPEPTIDE, QUINOXALINE, THIOACETAL, ANTIBIOTIC, ANTITUMOR, DNA-ANTIBIOTIC COMPLEX' # 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 4 ? E N N 4 ? F N N 5 ? G N N 5 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 PDB 1PFE 1 ? ? 1PFE ? 2 NOR NOR01126 2 ? ? NOR01126 ? # 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 1PFE A 1 ? 8 ? 1PFE 1 ? 8 ? 1 8 2 2 1PFE B 1 ? 8 ? NOR01126 1 ? 8 ? 1 8 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 2 1PFE N2C B 3 ? NOR NOR01126 NCY 3 microheterogeneity 3 1 2 1PFE NCY B 7 ? NOR NOR01126 N2C 7 microheterogeneity 7 2 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # 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)' 730 ? 1 MORE -6.4 ? 1 'SSA (A^2)' 3960 ? # _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,D,E,F,G # 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' 9_555 -x,-x+y,-z -0.5000000000 -0.8660254038 0.0000000000 0.0000000000 -0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # _struct_biol.id 1 _struct_biol.details 'The second part of the biological assembly is generated by: -x, -x+y, -z' _struct_biol.pdbx_parent_biol_id ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? D QUI . C ? ? ? 1_555 B DSN 1 N ? ? B QUI 0 B DSN 1 1_555 ? ? ? ? ? ? ? 1.345 ? ? covale2 covale both ? B DSN 1 C ? ? ? 1_555 B ALA 2 N ? ? B DSN 1 B ALA 2 1_555 ? ? ? ? ? ? ? 1.352 ? ? covale3 covale one ? B DSN 1 OG ? ? ? 1_555 B MVA 8 C ? ? B DSN 1 B MVA 8 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale4 covale both ? B ALA 2 C ? ? ? 1_555 B N2C 3 N A ? B ALA 2 B N2C 3 1_555 ? ? ? ? ? ? ? 1.355 ? ? covale5 covale both ? B ALA 2 C ? ? ? 1_555 B NCY 3 N B ? B ALA 2 B NCY 3 1_555 ? ? ? ? ? ? ? 1.355 ? ? covale6 covale both ? B NCY 3 C B ? ? 1_555 B MVA 4 N ? ? B NCY 3 B MVA 4 1_555 ? ? ? ? ? ? ? 1.338 ? ? covale7 covale both ? B N2C 3 C A ? ? 1_555 B MVA 4 N ? ? B N2C 3 B MVA 4 1_555 ? ? ? ? ? ? ? 1.338 ? ? covale8 covale both ? B N2C 3 CB A ? ? 1_555 B NCY 7 SG A ? B N2C 3 B NCY 7 1_555 ? ? ? ? ? ? ? 1.796 ? ? covale9 covale both ? B NCY 3 SG B ? ? 1_555 B N2C 7 CB B ? B NCY 3 B N2C 7 1_555 ? ? ? ? ? ? ? 1.814 ? ? covale10 covale one ? B MVA 4 C ? ? ? 1_555 B DSN 5 OG ? ? B MVA 4 B DSN 5 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale11 covale both ? B DSN 5 C ? ? ? 1_555 B ALA 6 N ? ? B DSN 5 B ALA 6 1_555 ? ? ? ? ? ? ? 1.317 ? ? covale12 covale both ? B DSN 5 N ? ? ? 1_555 E QUI . C ? ? B DSN 5 B QUI 9 1_555 ? ? ? ? ? ? ? 1.365 ? ? covale13 covale both ? B ALA 6 C ? ? ? 1_555 B NCY 7 N A ? B ALA 6 B NCY 7 1_555 ? ? ? ? ? ? ? 1.354 ? ? covale14 covale both ? B ALA 6 C ? ? ? 1_555 B N2C 7 N B ? B ALA 6 B N2C 7 1_555 ? ? ? ? ? ? ? 1.354 ? ? covale15 covale both ? B NCY 7 C A ? ? 1_555 B MVA 8 N ? ? B NCY 7 B MVA 8 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale16 covale both ? B N2C 7 C B ? ? 1_555 B MVA 8 N ? ? B N2C 7 B MVA 8 1_555 ? ? ? ? ? ? ? 1.323 ? ? hydrog1 hydrog ? ? A DG 1 O6 ? ? ? 1_555 A DC 8 N4 ? ? A DG 1 A DC 8 9_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog2 hydrog ? ? A DC 2 N3 ? ? ? 1_555 A DG 7 N1 ? ? A DC 2 A DG 7 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 2 N4 ? ? ? 1_555 A DG 7 O6 ? ? A DC 2 A DG 7 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 O2 ? ? ? 1_555 A DG 7 N2 ? ? A DC 2 A DG 7 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 3 N1 ? ? ? 1_555 A DC 6 N3 ? ? A DG 3 A DC 6 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DC 6 O2 ? ? A DG 3 A DC 6 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 O6 ? ? ? 1_555 A DC 6 N4 ? ? A DG 3 A DC 6 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 4 N3 ? ? ? 1_555 A DA 5 N7 ? ? A DT 4 A DA 5 9_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog9 hydrog ? ? A DT 4 O4 ? ? ? 1_555 A DA 5 N6 ? ? A DT 4 A DA 5 9_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog10 hydrog ? ? A DA 5 N6 ? ? ? 1_555 A DT 4 O4 ? ? A DA 5 A DT 4 9_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog11 hydrog ? ? A DA 5 N7 ? ? ? 1_555 A DT 4 N3 ? ? A DA 5 A DT 4 9_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog12 hydrog ? ? A DC 6 N3 ? ? ? 1_555 A DG 3 N1 ? ? A DC 6 A DG 3 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 6 N4 ? ? ? 1_555 A DG 3 O6 ? ? A DC 6 A DG 3 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 6 O2 ? ? ? 1_555 A DG 3 N2 ? ? A DC 6 A DG 3 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 7 N1 ? ? ? 1_555 A DC 2 N3 ? ? A DG 7 A DC 2 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 7 N2 ? ? ? 1_555 A DC 2 O2 ? ? A DG 7 A DC 2 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 7 O6 ? ? ? 1_555 A DC 2 N4 ? ? A DG 7 A DC 2 9_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 N4 ? ? ? 1_555 A DG 1 O6 ? ? A DC 8 A DG 1 9_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A CL 20 ? 1 'BINDING SITE FOR RESIDUE CL A 20' AC2 Software ? ? ? ? 16 'BINDING SITE FOR CHAIN B OF ECHINOMYCIN' 1 ? ? ? ? ? ? ? # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 1 HOH F . ? HOH A 2069 . ? 1_555 ? 2 AC2 16 DG A 1 ? DG A 1 . ? 1_555 ? 3 AC2 16 DC A 2 ? DC A 2 . ? 1_555 ? 4 AC2 16 DG A 3 ? DG A 3 . ? 1_555 ? 5 AC2 16 DT A 4 ? DT A 4 . ? 1_555 ? 6 AC2 16 DA A 5 ? DA A 5 . ? 1_555 ? 7 AC2 16 DC A 6 ? DC A 6 . ? 1_555 ? 8 AC2 16 DG A 7 ? DG A 7 . ? 1_555 ? 9 AC2 16 DC A 8 ? DC A 8 . ? 1_555 ? 10 AC2 16 HOH G . ? HOH B 2001 . ? 1_555 ? 11 AC2 16 HOH G . ? HOH B 2002 . ? 1_555 ? 12 AC2 16 HOH G . ? HOH B 2003 . ? 1_555 ? 13 AC2 16 HOH G . ? HOH B 2005 . ? 1_555 ? 14 AC2 16 HOH G . ? HOH B 2006 . ? 1_555 ? 15 AC2 16 HOH G . ? HOH B 2007 . ? 1_555 ? 16 AC2 16 HOH G . ? HOH B 2009 . ? 1_555 ? 17 AC2 16 HOH G . ? HOH B 2010 . ? 1_555 ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "C2'" A DG 1 ? A "C1'" A DG 1 ? ? 1.441 1.518 -0.077 0.010 N 2 1 "O4'" A DG 1 ? ? "C1'" A DG 1 ? ? 1.531 1.420 0.111 0.011 N 3 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? 1.506 1.420 0.086 0.011 N 4 1 "C2'" A DG 3 ? ? "C1'" A DG 3 ? ? 1.597 1.519 0.078 0.010 N 5 1 "O4'" A DG 3 ? ? "C1'" A DG 3 ? ? 1.332 1.418 -0.086 0.012 N 6 1 "O4'" A DT 4 ? ? "C1'" A DT 4 ? ? 1.499 1.420 0.079 0.011 N 7 1 "C2'" A DG 7 ? ? "C1'" A DG 7 ? ? 1.595 1.519 0.076 0.010 N 8 1 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? 1.339 1.418 -0.079 0.012 N 9 1 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? 1.505 1.420 0.085 0.011 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 99.34 108.00 -8.66 0.70 N 2 1 "C5'" A DC 2 ? B "C4'" A DC 2 ? B "O4'" A DC 2 ? ? 119.18 109.80 9.38 1.10 N 3 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 102.50 108.00 -5.50 0.70 N 4 1 "O4'" A DG 3 ? ? "C1'" A DG 3 ? ? N9 A DG 3 ? ? 115.21 108.30 6.91 0.30 N 5 1 "O4'" A DT 4 ? ? "C1'" A DT 4 ? ? N1 A DT 4 ? ? 101.66 108.00 -6.34 0.70 N 6 1 "C1'" A DA 5 ? ? "O4'" A DA 5 ? ? "C4'" A DA 5 ? ? 103.39 110.10 -6.71 1.00 N 7 1 "O4'" A DC 6 ? ? "C1'" A DC 6 ? ? N1 A DC 6 ? ? 102.26 108.00 -5.74 0.70 N 8 1 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 114.52 108.30 6.22 0.30 N 9 1 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 102.82 108.00 -5.18 0.70 N 10 1 N3 A DC 8 ? ? C4 A DC 8 ? ? C5 A DC 8 ? ? 118.62 121.90 -3.28 0.40 N 11 1 N1 A DC 8 ? ? C2 A DC 8 ? ? O2 A DC 8 ? ? 123.67 118.90 4.77 0.60 N # _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 B 1 PRD_000491 D 1 PRD_000491 E # _struct_site_keywords.site_id 1 _struct_site_keywords.text Intercalation # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 2002 ? F HOH . 2 1 A HOH 2013 ? F HOH . 3 1 A HOH 2019 ? F HOH . 4 1 A HOH 2024 ? F HOH . # _pdbx_entry_details.entry_id 1PFE _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.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.has_ligand_of_interest ? # 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 ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 CL CL CL N N 14 DA OP3 O N N 15 DA P P N N 16 DA OP1 O N N 17 DA OP2 O N N 18 DA "O5'" O N N 19 DA "C5'" C N N 20 DA "C4'" C N R 21 DA "O4'" O N N 22 DA "C3'" C N S 23 DA "O3'" O N N 24 DA "C2'" C N N 25 DA "C1'" C N R 26 DA N9 N Y N 27 DA C8 C Y N 28 DA N7 N Y N 29 DA C5 C Y N 30 DA C6 C Y N 31 DA N6 N N N 32 DA N1 N Y N 33 DA C2 C Y N 34 DA N3 N Y N 35 DA C4 C Y N 36 DA HOP3 H N N 37 DA HOP2 H N N 38 DA "H5'" H N N 39 DA "H5''" H N N 40 DA "H4'" H N N 41 DA "H3'" H N N 42 DA "HO3'" H N N 43 DA "H2'" H N N 44 DA "H2''" H N N 45 DA "H1'" H N N 46 DA H8 H N N 47 DA H61 H N N 48 DA H62 H N N 49 DA H2 H N N 50 DC OP3 O N N 51 DC P P N N 52 DC OP1 O N N 53 DC OP2 O N N 54 DC "O5'" O N N 55 DC "C5'" C N N 56 DC "C4'" C N R 57 DC "O4'" O N N 58 DC "C3'" C N S 59 DC "O3'" O N N 60 DC "C2'" C N N 61 DC "C1'" C N R 62 DC N1 N N N 63 DC C2 C N N 64 DC O2 O N N 65 DC N3 N N N 66 DC C4 C N N 67 DC N4 N N N 68 DC C5 C N N 69 DC C6 C N N 70 DC HOP3 H N N 71 DC HOP2 H N N 72 DC "H5'" H N N 73 DC "H5''" H N N 74 DC "H4'" H N N 75 DC "H3'" H N N 76 DC "HO3'" H N N 77 DC "H2'" H N N 78 DC "H2''" H N N 79 DC "H1'" H N N 80 DC H41 H N N 81 DC H42 H N N 82 DC H5 H N N 83 DC H6 H N N 84 DG OP3 O N N 85 DG P P N N 86 DG OP1 O N N 87 DG OP2 O N N 88 DG "O5'" O N N 89 DG "C5'" C N N 90 DG "C4'" C N R 91 DG "O4'" O N N 92 DG "C3'" C N S 93 DG "O3'" O N N 94 DG "C2'" C N N 95 DG "C1'" C N R 96 DG N9 N Y N 97 DG C8 C Y N 98 DG N7 N Y N 99 DG C5 C Y N 100 DG C6 C N N 101 DG O6 O N N 102 DG N1 N N N 103 DG C2 C N N 104 DG N2 N N N 105 DG N3 N N N 106 DG C4 C Y N 107 DG HOP3 H N N 108 DG HOP2 H N N 109 DG "H5'" H N N 110 DG "H5''" H N N 111 DG "H4'" H N N 112 DG "H3'" H N N 113 DG "HO3'" H N N 114 DG "H2'" H N N 115 DG "H2''" H N N 116 DG "H1'" H N N 117 DG H8 H N N 118 DG H1 H N N 119 DG H21 H N N 120 DG H22 H N N 121 DSN N N N N 122 DSN CA C N R 123 DSN C C N N 124 DSN O O N N 125 DSN OXT O N N 126 DSN CB C N N 127 DSN OG O N N 128 DSN H H N N 129 DSN H2 H N N 130 DSN HA H N N 131 DSN HXT H N N 132 DSN HB2 H N N 133 DSN HB3 H N N 134 DSN HG H N N 135 DT OP3 O N N 136 DT P P N N 137 DT OP1 O N N 138 DT OP2 O N N 139 DT "O5'" O N N 140 DT "C5'" C N N 141 DT "C4'" C N R 142 DT "O4'" O N N 143 DT "C3'" C N S 144 DT "O3'" O N N 145 DT "C2'" C N N 146 DT "C1'" C N R 147 DT N1 N N N 148 DT C2 C N N 149 DT O2 O N N 150 DT N3 N N N 151 DT C4 C N N 152 DT O4 O N N 153 DT C5 C N N 154 DT C7 C N N 155 DT C6 C N N 156 DT HOP3 H N N 157 DT HOP2 H N N 158 DT "H5'" H N N 159 DT "H5''" H N N 160 DT "H4'" H N N 161 DT "H3'" H N N 162 DT "HO3'" H N N 163 DT "H2'" H N N 164 DT "H2''" H N N 165 DT "H1'" H N N 166 DT H3 H N N 167 DT H71 H N N 168 DT H72 H N N 169 DT H73 H N N 170 DT H6 H N N 171 HOH O O N N 172 HOH H1 H N N 173 HOH H2 H N N 174 MVA N N N N 175 MVA CN C N N 176 MVA CA C N S 177 MVA CB C N N 178 MVA CG1 C N N 179 MVA CG2 C N N 180 MVA C C N N 181 MVA O O N N 182 MVA OXT O N N 183 MVA H H N N 184 MVA HN1 H N N 185 MVA HN2 H N N 186 MVA HN3 H N N 187 MVA HA H N N 188 MVA HB H N N 189 MVA HG11 H N N 190 MVA HG12 H N N 191 MVA HG13 H N N 192 MVA HG21 H N N 193 MVA HG22 H N N 194 MVA HG23 H N N 195 MVA HXT H N N 196 N2C N N N N 197 N2C CA C N R 198 N2C CB C N N 199 N2C SG S N N 200 N2C CD C N N 201 N2C CN C N N 202 N2C C C N N 203 N2C O O N N 204 N2C OXT O N N 205 N2C H H N N 206 N2C HA H N N 207 N2C HB2 H N N 208 N2C HB3 H N N 209 N2C HD1 H N N 210 N2C HD2 H N N 211 N2C HD3 H N N 212 N2C HN1 H N N 213 N2C HN2 H N N 214 N2C HN3 H N N 215 N2C HXT H N N 216 NCY N N N N 217 NCY CA C N R 218 NCY CB C N N 219 NCY SG S N N 220 NCY CN C N N 221 NCY C C N N 222 NCY O O N N 223 NCY OXT O N N 224 NCY H H N N 225 NCY HA H N N 226 NCY HB2 H N N 227 NCY HB3 H N N 228 NCY HG H N N 229 NCY HCN1 H N N 230 NCY HCN2 H N N 231 NCY HCN3 H N N 232 NCY HXT H N N 233 QUI N1 N Y N 234 QUI C2 C Y N 235 QUI C3 C Y N 236 QUI N4 N Y N 237 QUI C5 C Y N 238 QUI C6 C Y N 239 QUI C7 C Y N 240 QUI C8 C Y N 241 QUI C9 C Y N 242 QUI C10 C Y N 243 QUI C C N N 244 QUI O1 O N N 245 QUI O2 O N N 246 QUI H3 H N N 247 QUI H5 H N N 248 QUI H6 H N N 249 QUI H7 H N N 250 QUI H8 H N N 251 QUI HO2 H N N 252 # 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 ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 DA OP3 P sing N N 13 DA OP3 HOP3 sing N N 14 DA P OP1 doub N N 15 DA P OP2 sing N N 16 DA P "O5'" sing N N 17 DA OP2 HOP2 sing N N 18 DA "O5'" "C5'" sing N N 19 DA "C5'" "C4'" sing N N 20 DA "C5'" "H5'" sing N N 21 DA "C5'" "H5''" sing N N 22 DA "C4'" "O4'" sing N N 23 DA "C4'" "C3'" sing N N 24 DA "C4'" "H4'" sing N N 25 DA "O4'" "C1'" sing N N 26 DA "C3'" "O3'" sing N N 27 DA "C3'" "C2'" sing N N 28 DA "C3'" "H3'" sing N N 29 DA "O3'" "HO3'" sing N N 30 DA "C2'" "C1'" sing N N 31 DA "C2'" "H2'" sing N N 32 DA "C2'" "H2''" sing N N 33 DA "C1'" N9 sing N N 34 DA "C1'" "H1'" sing N N 35 DA N9 C8 sing Y N 36 DA N9 C4 sing Y N 37 DA C8 N7 doub Y N 38 DA C8 H8 sing N N 39 DA N7 C5 sing Y N 40 DA C5 C6 sing Y N 41 DA C5 C4 doub Y N 42 DA C6 N6 sing N N 43 DA C6 N1 doub Y N 44 DA N6 H61 sing N N 45 DA N6 H62 sing N N 46 DA N1 C2 sing Y N 47 DA C2 N3 doub Y N 48 DA C2 H2 sing N N 49 DA N3 C4 sing Y N 50 DC OP3 P sing N N 51 DC OP3 HOP3 sing N N 52 DC P OP1 doub N N 53 DC P OP2 sing N N 54 DC P "O5'" sing N N 55 DC OP2 HOP2 sing N N 56 DC "O5'" "C5'" sing N N 57 DC "C5'" "C4'" sing N N 58 DC "C5'" "H5'" sing N N 59 DC "C5'" "H5''" sing N N 60 DC "C4'" "O4'" sing N N 61 DC "C4'" "C3'" sing N N 62 DC "C4'" "H4'" sing N N 63 DC "O4'" "C1'" sing N N 64 DC "C3'" "O3'" sing N N 65 DC "C3'" "C2'" sing N N 66 DC "C3'" "H3'" sing N N 67 DC "O3'" "HO3'" sing N N 68 DC "C2'" "C1'" sing N N 69 DC "C2'" "H2'" sing N N 70 DC "C2'" "H2''" sing N N 71 DC "C1'" N1 sing N N 72 DC "C1'" "H1'" sing N N 73 DC N1 C2 sing N N 74 DC N1 C6 sing N N 75 DC C2 O2 doub N N 76 DC C2 N3 sing N N 77 DC N3 C4 doub N N 78 DC C4 N4 sing N N 79 DC C4 C5 sing N N 80 DC N4 H41 sing N N 81 DC N4 H42 sing N N 82 DC C5 C6 doub N N 83 DC C5 H5 sing N N 84 DC C6 H6 sing N N 85 DG OP3 P sing N N 86 DG OP3 HOP3 sing N N 87 DG P OP1 doub N N 88 DG P OP2 sing N N 89 DG P "O5'" sing N N 90 DG OP2 HOP2 sing N N 91 DG "O5'" "C5'" sing N N 92 DG "C5'" "C4'" sing N N 93 DG "C5'" "H5'" sing N N 94 DG "C5'" "H5''" sing N N 95 DG "C4'" "O4'" sing N N 96 DG "C4'" "C3'" sing N N 97 DG "C4'" "H4'" sing N N 98 DG "O4'" "C1'" sing N N 99 DG "C3'" "O3'" sing N N 100 DG "C3'" "C2'" sing N N 101 DG "C3'" "H3'" sing N N 102 DG "O3'" "HO3'" sing N N 103 DG "C2'" "C1'" sing N N 104 DG "C2'" "H2'" sing N N 105 DG "C2'" "H2''" sing N N 106 DG "C1'" N9 sing N N 107 DG "C1'" "H1'" sing N N 108 DG N9 C8 sing Y N 109 DG N9 C4 sing Y N 110 DG C8 N7 doub Y N 111 DG C8 H8 sing N N 112 DG N7 C5 sing Y N 113 DG C5 C6 sing N N 114 DG C5 C4 doub Y N 115 DG C6 O6 doub N N 116 DG C6 N1 sing N N 117 DG N1 C2 sing N N 118 DG N1 H1 sing N N 119 DG C2 N2 sing N N 120 DG C2 N3 doub N N 121 DG N2 H21 sing N N 122 DG N2 H22 sing N N 123 DG N3 C4 sing N N 124 DSN N CA sing N N 125 DSN N H sing N N 126 DSN N H2 sing N N 127 DSN CA C sing N N 128 DSN CA CB sing N N 129 DSN CA HA sing N N 130 DSN C O doub N N 131 DSN C OXT sing N N 132 DSN OXT HXT sing N N 133 DSN CB OG sing N N 134 DSN CB HB2 sing N N 135 DSN CB HB3 sing N N 136 DSN OG HG sing N N 137 DT OP3 P sing N N 138 DT OP3 HOP3 sing N N 139 DT P OP1 doub N N 140 DT P OP2 sing N N 141 DT P "O5'" sing N N 142 DT OP2 HOP2 sing N N 143 DT "O5'" "C5'" sing N N 144 DT "C5'" "C4'" sing N N 145 DT "C5'" "H5'" sing N N 146 DT "C5'" "H5''" sing N N 147 DT "C4'" "O4'" sing N N 148 DT "C4'" "C3'" sing N N 149 DT "C4'" "H4'" sing N N 150 DT "O4'" "C1'" sing N N 151 DT "C3'" "O3'" sing N N 152 DT "C3'" "C2'" sing N N 153 DT "C3'" "H3'" sing N N 154 DT "O3'" "HO3'" sing N N 155 DT "C2'" "C1'" sing N N 156 DT "C2'" "H2'" sing N N 157 DT "C2'" "H2''" sing N N 158 DT "C1'" N1 sing N N 159 DT "C1'" "H1'" sing N N 160 DT N1 C2 sing N N 161 DT N1 C6 sing N N 162 DT C2 O2 doub N N 163 DT C2 N3 sing N N 164 DT N3 C4 sing N N 165 DT N3 H3 sing N N 166 DT C4 O4 doub N N 167 DT C4 C5 sing N N 168 DT C5 C7 sing N N 169 DT C5 C6 doub N N 170 DT C7 H71 sing N N 171 DT C7 H72 sing N N 172 DT C7 H73 sing N N 173 DT C6 H6 sing N N 174 HOH O H1 sing N N 175 HOH O H2 sing N N 176 MVA N CN sing N N 177 MVA N CA sing N N 178 MVA N H sing N N 179 MVA CN HN1 sing N N 180 MVA CN HN2 sing N N 181 MVA CN HN3 sing N N 182 MVA CA CB sing N N 183 MVA CA C sing N N 184 MVA CA HA sing N N 185 MVA CB CG1 sing N N 186 MVA CB CG2 sing N N 187 MVA CB HB sing N N 188 MVA CG1 HG11 sing N N 189 MVA CG1 HG12 sing N N 190 MVA CG1 HG13 sing N N 191 MVA CG2 HG21 sing N N 192 MVA CG2 HG22 sing N N 193 MVA CG2 HG23 sing N N 194 MVA C O doub N N 195 MVA C OXT sing N N 196 MVA OXT HXT sing N N 197 N2C N CA sing N N 198 N2C N CN sing N N 199 N2C N H sing N N 200 N2C CA CB sing N N 201 N2C CA C sing N N 202 N2C CA HA sing N N 203 N2C CB SG sing N N 204 N2C CB HB2 sing N N 205 N2C CB HB3 sing N N 206 N2C SG CD sing N N 207 N2C CD HD1 sing N N 208 N2C CD HD2 sing N N 209 N2C CD HD3 sing N N 210 N2C CN HN1 sing N N 211 N2C CN HN2 sing N N 212 N2C CN HN3 sing N N 213 N2C C O doub N N 214 N2C C OXT sing N N 215 N2C OXT HXT sing N N 216 NCY N CA sing N N 217 NCY N CN sing N N 218 NCY N H sing N N 219 NCY CA CB sing N N 220 NCY CA C sing N N 221 NCY CA HA sing N N 222 NCY CB SG sing N N 223 NCY CB HB2 sing N N 224 NCY CB HB3 sing N N 225 NCY SG HG sing N N 226 NCY CN HCN1 sing N N 227 NCY CN HCN2 sing N N 228 NCY CN HCN3 sing N N 229 NCY C O doub N N 230 NCY C OXT sing N N 231 NCY OXT HXT sing N N 232 QUI N1 C2 doub Y N 233 QUI N1 C9 sing Y N 234 QUI C2 C3 sing Y N 235 QUI C2 C sing N N 236 QUI C3 N4 doub Y N 237 QUI C3 H3 sing N N 238 QUI N4 C10 sing Y N 239 QUI C5 C6 doub Y N 240 QUI C5 C10 sing Y N 241 QUI C5 H5 sing N N 242 QUI C6 C7 sing Y N 243 QUI C6 H6 sing N N 244 QUI C7 C8 doub Y N 245 QUI C7 H7 sing N N 246 QUI C8 C9 sing Y N 247 QUI C8 H8 sing N N 248 QUI C9 C10 doub Y N 249 QUI C O1 doub N N 250 QUI C O2 sing N N 251 QUI O2 HO2 sing N N 252 # _ndb_struct_conf_na.entry_id 1PFE _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 DG 1 1_555 A DC 8 9_555 0.445 -3.489 -0.388 4.097 -4.685 66.359 1 A_DG1:DC8_A A 1 ? A 8 ? ? ? 1 A DG 1 1_555 A DC 8 1_555 0.445 -3.489 -0.388 4.097 -4.685 66.359 2 A_DG1:DC8_A A 1 ? A 8 ? ? ? 1 A DC 2 1_555 A DG 7 9_555 0.376 -0.127 0.312 -23.917 6.552 -1.666 3 A_DC2:DG7_A A 2 ? A 7 ? 19 1 1 A DG 3 1_555 A DC 6 9_555 -0.350 -0.080 0.358 23.129 7.146 -0.062 4 A_DG3:DC6_A A 3 ? A 6 ? 19 1 1 A DT 4 1_555 A DA 5 9_555 -0.567 3.640 0.189 0.747 9.053 -67.135 5 A_DT4:DA5_A A 4 ? A 5 ? 23 3 1 A DA 5 1_555 A DT 4 9_555 0.567 -3.640 -0.189 -0.747 -9.053 67.135 6 A_DA5:DT4_A A 5 ? A 4 ? 23 3 1 A DC 6 1_555 A DG 3 9_555 0.350 -0.080 0.358 -23.129 7.146 -0.062 7 A_DC6:DG3_A A 6 ? A 3 ? 19 1 1 A DG 7 1_555 A DC 2 9_555 -0.376 -0.127 0.312 23.917 6.552 -1.666 8 A_DG7:DC2_A A 7 ? A 2 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 2 1_555 A DG 7 9_555 A DG 3 1_555 A DC 6 9_555 0.152 0.809 2.432 -1.150 2.248 -4.199 -21.547 -4.403 1.749 -27.621 -14.134 -4.899 1 AA_DC2DG3:DC6DG7_AA A 2 ? A 7 ? A 3 ? A 6 ? 1 A DG 3 1_555 A DC 6 9_555 A DT 4 1_555 A DA 5 9_555 0.307 -0.059 7.183 -5.488 8.186 65.388 -0.779 -0.767 7.090 7.533 5.050 66.045 2 AA_DG3DT4:DA5DC6_AA A 3 ? A 6 ? A 4 ? A 5 ? 1 A DT 4 1_555 A DA 5 9_555 A DA 5 1_555 A DT 4 9_555 2.940 -5.003 0.000 -151.053 78.005 180.000 -2.501 -1.470 0.000 39.003 75.527 180.000 3 AA_DT4DA5:DT4DA5_AA A 4 ? A 5 ? A 5 ? A 4 ? 1 A DA 5 1_555 A DT 4 9_555 A DC 6 1_555 A DG 3 9_555 3.695 6.164 -0.222 -143.188 91.904 -112.324 -3.042 1.917 -0.307 -46.401 -72.294 -174.517 4 AA_DA5DC6:DG3DT4_AA A 5 ? A 4 ? A 6 ? A 3 ? 1 A DC 6 1_555 A DG 3 9_555 A DG 7 1_555 A DC 2 9_555 -0.152 0.809 2.432 1.150 2.248 -4.199 -21.547 4.403 1.749 -27.621 14.134 -4.899 5 AA_DC6DG7:DC2DG3_AA A 6 ? A 3 ? A 7 ? A 2 ? # _pdbx_initial_refinement_model.accession_code ? _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 Other _pdbx_initial_refinement_model.details 'TROSTIN A - (GCGTACGC)2 COMPLEX' # _atom_sites.entry_id 1PFE _atom_sites.fract_transf_matrix[1][1] 0.025397 _atom_sites.fract_transf_matrix[1][2] 0.014663 _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] 0.029326 _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] 0.012542 _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 CL N O P S # loop_