data_8DVY # _model_server_result.job_id XNhRCg_6z9q1Pf35FeSWMQ _model_server_result.datetime_utc '2024-11-22 14:16:50' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 8dvy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 8DVY # _exptl.entry_id 8DVY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 351.64 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'IRON/SULFUR CLUSTER' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 8DVY _cell.length_a 37.86 _cell.length_b 85.48 _cell.length_c 140.71 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DVY _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _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 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_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_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 B O3' DC 5 B DC 5 1_555 B P 8OG 6 B 8OG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? covale ? covale2 B O3' 8OG 6 B 8OG 6 1_555 B P DT 7 B DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.595 ? covale ? covale3 C O3' DA 6 C DA 17 1_555 C P AAB 7 C AAB 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? covale ? covale4 C O3' AAB 7 C AAB 18 1_555 C P DG 8 C DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.63 ? metalc ? metalc1 A O SER 118 A SER 118 1_555 F CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc2 A OG SER 118 A SER 118 1_555 F CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.611 ? metalc ? metalc3 A O VAL 123 A VAL 123 1_555 F CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc4 A OD2 ASP 144 A ASP 144 1_555 H CA CA . C CA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.687 ? metalc ? metalc5 A OG SER 146 A SER 146 1_555 H CA CA . C CA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc6 A SG CYS 198 A CYS 198 1_555 D FE3 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc7 A SG CYS 205 A CYS 205 1_555 D FE2 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc8 A SG CYS 208 A CYS 208 1_555 D FE1 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc9 A SG CYS 214 A CYS 214 1_555 D FE4 SF4 . A SF4 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc10 A OD2 ASP 257 A ASP 257 1_555 G CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? metalc ? metalc11 A O THR 259 A THR 259 1_555 G CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc12 A OG1 THR 259 A THR 259 1_555 G CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.712 ? metalc ? metalc13 F CA CA . A CA 403 1_555 I O HOH . A HOH 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc14 F CA CA . A CA 403 1_555 I O HOH . A HOH 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc15 I O HOH . A HOH 509 1_555 H CA CA . C CA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc16 C O4' AAB 7 C AAB 18 1_555 H CA CA . C CA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? metalc ? metalc17 C O3' AAB 7 C AAB 18 1_555 H CA CA . C CA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.079 ? hydrog WATSON-CRICK hydrog1 B N1 DA 2 B DA 2 1_555 C N3 DT 11 C DT 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N6 DA 2 B DA 2 1_555 C O4 DT 11 C DT 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N1 DG 3 B DG 3 1_555 C N3 DC 10 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N2 DG 3 B DG 3 1_555 C O2 DC 10 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O6 DG 3 B DG 3 1_555 C N4 DC 10 C DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 DA 4 B DA 4 1_555 C N3 DT 9 C DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N6 DA 4 B DA 4 1_555 C O4 DT 9 C DT 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N3 DC 5 B DC 5 1_555 C N1 DG 8 C DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N4 DC 5 B DC 5 1_555 C O6 DG 8 C DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O2 DC 5 B DC 5 1_555 C N2 DG 8 C DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N3 DT 7 B DT 7 1_555 C N1 DA 6 C DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B O4 DT 7 B DT 7 1_555 C N6 DA 6 C DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N1 DG 8 B DG 8 1_555 C N3 DC 5 C DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N2 DG 8 B DG 8 1_555 C O2 DC 5 C DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O6 DG 8 B DG 8 1_555 C N4 DC 5 C DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N1 DG 9 B DG 9 1_555 C N3 DC 4 C DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N2 DG 9 B DG 9 1_555 C O2 DC 4 C DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O6 DG 9 B DG 9 1_555 C N4 DC 4 C DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N1 DA 10 B DA 10 1_555 C N3 DT 3 C DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N6 DA 10 B DA 10 1_555 C O4 DT 3 C DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N3 DC 11 B DC 11 1_555 C N1 DG 2 C DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N4 DC 11 B DC 11 1_555 C O6 DG 2 C DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B O2 DC 11 B DC 11 1_555 C N2 DG 2 C DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'Fe4 S4' _chem_comp.formula_weight 351.64 _chem_comp.id SF4 _chem_comp.mon_nstd_flag . _chem_comp.name 'IRON/SULFUR CLUSTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag FE1 S2 SF4 sing 509 n n FE1 S3 SF4 sing 510 n n FE1 S4 SF4 sing 511 n n FE2 S1 SF4 sing 512 n n FE2 S3 SF4 sing 513 n n FE2 S4 SF4 sing 514 n n FE3 S1 SF4 sing 515 n n FE3 S2 SF4 sing 516 n n FE3 S4 SF4 sing 517 n n FE4 S1 SF4 sing 518 n n FE4 S2 SF4 sing 519 n n FE4 S3 SF4 sing 520 n n # _atom_sites.entry_id 8DVY _atom_sites.fract_transf_matrix[1][1] 0.026413 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011699 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.007107 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_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_ins_code D 4 SF4 A 1 401 401 SF4 SF4 . E 5 ACT A 1 402 402 ACT ACT . F 6 CA A 1 403 1 CA CA . G 6 CA A 1 404 3 CA CA . H 6 CA C 1 101 2 CA CA . I 7 HOH A 1 501 34 HOH HOH . I 7 HOH A 2 502 26 HOH HOH . I 7 HOH A 3 503 18 HOH HOH . I 7 HOH A 4 504 28 HOH HOH . I 7 HOH A 5 505 29 HOH HOH . I 7 HOH A 6 506 36 HOH HOH . I 7 HOH A 7 507 5 HOH HOH . I 7 HOH A 8 508 41 HOH HOH . I 7 HOH A 9 509 1 HOH HOH . I 7 HOH A 10 510 25 HOH HOH . I 7 HOH A 11 511 2 HOH HOH . I 7 HOH A 12 512 3 HOH HOH . I 7 HOH A 13 513 16 HOH HOH . I 7 HOH A 14 514 33 HOH HOH . I 7 HOH A 15 515 13 HOH HOH . I 7 HOH A 16 516 14 HOH HOH . I 7 HOH A 17 517 24 HOH HOH . I 7 HOH A 18 518 40 HOH HOH . I 7 HOH A 19 519 31 HOH HOH . J 7 HOH B 1 101 37 HOH HOH . K 7 HOH C 1 201 35 HOH HOH . K 7 HOH C 2 202 38 HOH HOH . K 7 HOH C 3 203 39 HOH HOH . K 7 HOH C 4 204 15 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 FE FE1 SF4 . . . D 4 7.924 -14.011 -2.304 1 48.66 ? FE1 SF4 401 A 1 HETATM 2 FE FE2 SF4 . . . D 4 8.497 -16.307 -0.951 1 47.62 ? FE2 SF4 401 A 1 HETATM 3 FE FE3 SF4 . . . D 4 9.923 -13.996 -0.461 1 52.87 ? FE3 SF4 401 A 1 HETATM 4 FE FE4 SF4 . . . D 4 10.284 -15.331 -2.756 1 52.54 ? FE4 SF4 401 A 1 HETATM 5 S S1 SF4 . . . D 4 10.765 -16.107 -0.674 1 46.23 ? S1 SF4 401 A 1 HETATM 6 S S2 SF4 . . . D 4 9.997 -13.08 -2.53 1 46.29 ? S2 SF4 401 A 1 HETATM 7 S S3 SF4 . . . D 4 8.176 -16.101 -3.157 1 48.58 ? S3 SF4 401 A 1 HETATM 8 S S4 SF4 . . . D 4 7.686 -14.365 -0.081 1 51.83 ? S4 SF4 401 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 8 #