data_2WDV # _model_server_result.job_id q_oG8GW38IpUj29r2gBqQA _model_server_result.datetime_utc '2024-11-27 10:16:16' _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 2wdv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":304}' # _entry.id 2WDV # _exptl.entry_id 2WDV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 295.795 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'FE3-S4 CLUSTER' _entity.pdbx_number_of_molecules 3 _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 2WDV _cell.length_a 120.34 _cell.length_b 184.847 _cell.length_c 204.72 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2WDV _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 PISA tetrameric 4 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,M,N,O,P,Q,R,S 1 1 E,F,G,H,T,U,V,W,X,Y,Z 2 1 I,J,K,L,AA,BA,CA,DA,EA,FA,GA 3 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 10 R N N ? 10 Y N N ? 10 FA N 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 A NE2 HIS 45 A HIS 45 1_555 M C8M FAD . A FAD 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.49 ? covale ? covale2 E NE2 HIS 45 E HIS 45 1_555 T C8M FAD . E FAD 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.508 ? covale ? covale3 I NE2 HIS 45 I HIS 45 1_555 AA C8M FAD . I FAD 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? metalc ? metalc1 A O MET 356 A MET 356 1_555 O NA NA . A NA 1590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? metalc ? metalc2 A O GLY 358 A GLY 358 1_555 O NA NA . A NA 1590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc3 A O GLU 388 A GLU 388 1_555 O NA NA . A NA 1590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc4 A O ALA 390 A ALA 390 1_555 O NA NA . A NA 1590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc5 B SG CYS 55 B CYS 55 1_555 P FE1 FES . B FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc6 B SG CYS 60 B CYS 60 1_555 P FE1 FES . B FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc7 B OD1 ASP 63 B ASP 63 1_555 P FE2 FES . B FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.823 ? metalc ? metalc8 B SG CYS 75 B CYS 75 1_555 P FE2 FES . B FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc9 B SG CYS 149 B CYS 149 1_555 Q FE3 SF4 . B SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc10 B SG CYS 152 B CYS 152 1_555 Q FE4 SF4 . B SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc11 B SG CYS 155 B CYS 155 1_555 Q FE1 SF4 . B SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc12 B SG CYS 159 B CYS 159 1_555 R FE1 F3S . B F3S 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc13 B SG CYS 206 B CYS 206 1_555 R FE3 F3S . B F3S 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc14 B SG CYS 212 B CYS 212 1_555 R FE4 F3S . B F3S 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc15 B SG CYS 216 B CYS 216 1_555 Q FE2 SF4 . B SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc16 C NE2 HIS 84 C HIS 84 1_555 S FE HEM . C HEM 1129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? metalc ? metalc17 S FE HEM . C HEM 1129 1_555 D NE2 HIS 71 D HIS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.93 ? metalc ? metalc18 E O MET 356 E MET 356 1_555 V NA NA . E NA 1590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc19 E O GLY 358 E GLY 358 1_555 V NA NA . E NA 1590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? metalc ? metalc20 E O GLU 388 E GLU 388 1_555 V NA NA . E NA 1590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.506 ? metalc ? metalc21 F SG CYS 55 F CYS 55 1_555 W FE1 FES . F FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc22 F SG CYS 60 F CYS 60 1_555 W FE1 FES . F FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc23 F OD1 ASP 63 F ASP 63 1_555 W FE2 FES . F FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.834 ? metalc ? metalc24 F SG CYS 75 F CYS 75 1_555 W FE2 FES . F FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc25 F SG CYS 149 F CYS 149 1_555 X FE2 SF4 . F SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc26 F SG CYS 152 F CYS 152 1_555 X FE3 SF4 . F SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc27 F SG CYS 155 F CYS 155 1_555 X FE1 SF4 . F SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc28 F SG CYS 159 F CYS 159 1_555 Y FE1 F3S . F F3S 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc29 F SG CYS 206 F CYS 206 1_555 Y FE3 F3S . F F3S 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc30 F SG CYS 212 F CYS 212 1_555 Y FE4 F3S . F F3S 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc31 F SG CYS 216 F CYS 216 1_555 X FE4 SF4 . F SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc32 G NE2 HIS 84 G HIS 84 1_555 Z FE HEM . G HEM 1129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? metalc ? metalc33 Z FE HEM . G HEM 1129 1_555 H NE2 HIS 71 H HIS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc34 J SG CYS 55 J CYS 55 1_555 DA FE1 FES . J FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc35 J SG CYS 60 J CYS 60 1_555 DA FE1 FES . J FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc36 J OD1 ASP 63 J ASP 63 1_555 DA FE2 FES . J FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.815 ? metalc ? metalc37 J OD2 ASP 63 J ASP 63 1_555 DA FE2 FES . J FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.711 ? metalc ? metalc38 J SG CYS 75 J CYS 75 1_555 DA FE2 FES . J FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc39 J SG CYS 149 J CYS 149 1_555 EA FE3 SF4 . J SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc40 J SG CYS 152 J CYS 152 1_555 EA FE4 SF4 . J SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc41 J SG CYS 155 J CYS 155 1_555 EA FE1 SF4 . J SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc42 J SG CYS 159 J CYS 159 1_555 FA FE1 F3S . J F3S 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc43 J SG CYS 206 J CYS 206 1_555 FA FE3 F3S . J F3S 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc44 J SG CYS 212 J CYS 212 1_555 FA FE4 F3S . J F3S 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc45 J SG CYS 216 J CYS 216 1_555 EA FE2 SF4 . J SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc46 K NE2 HIS 84 K HIS 84 1_555 GA FE HEM . K HEM 1129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? metalc ? metalc47 GA FE HEM . K HEM 1129 1_555 L NE2 HIS 71 L HIS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? # _chem_comp.formula 'Fe3 S4' _chem_comp.formula_weight 295.795 _chem_comp.id F3S _chem_comp.mon_nstd_flag . _chem_comp.name 'FE3-S4 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 S1 F3S sing 83 n n FE1 S2 F3S sing 84 n n FE1 S3 F3S sing 85 n n FE3 S1 F3S sing 86 n n FE3 S3 F3S sing 87 n n FE3 S4 F3S sing 88 n n FE4 S2 F3S sing 89 n n FE4 S3 F3S sing 90 n n FE4 S4 F3S sing 91 n n # _atom_sites.entry_id 2WDV _atom_sites.fract_transf_matrix[1][1] 0.00831 _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] 0.00541 _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] 0.004885 _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 M 5 FAD A 1 601 601 FAD FAD . N 6 TEO A 1 1589 1589 TEO TEO . O 7 NA A 1 1590 1590 NA NA . P 8 FES B 1 302 302 FES FES . Q 9 SF4 B 1 303 303 SF4 SF4 . R 10 F3S B 1 304 304 F3S F3S . S 11 HEM C 1 1129 1129 HEM HEM . T 5 FAD E 1 601 601 FAD FAD . U 6 TEO E 1 1589 1589 TEO TEO . V 7 NA E 1 1590 1590 NA NA . W 8 FES F 1 302 302 FES FES . X 9 SF4 F 1 303 303 SF4 SF4 . Y 10 F3S F 1 304 304 F3S F3S . Z 11 HEM G 1 1129 1129 HEM HEM . AA 5 FAD I 1 601 601 FAD FAD . BA 6 TEO I 1 1589 1589 TEO TEO . CA 7 NA I 1 1590 1590 NA NA . DA 8 FES J 1 302 302 FES FES . EA 9 SF4 J 1 303 303 SF4 SF4 . FA 10 F3S J 1 304 304 F3S F3S . GA 11 HEM K 1 1129 1129 HEM HEM . # 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 F3S . . . R 10 40.213 -10.047 -31.391 1 43.91 ? FE1 F3S 304 B 1 HETATM 2 FE FE3 F3S . . . R 10 41.416 -12.303 -30.269 1 49.78 ? FE3 F3S 304 B 1 HETATM 3 FE FE4 F3S . . . R 10 40.278 -10.658 -29.224 1 49.63 ? FE4 F3S 304 B 1 HETATM 4 S S1 F3S . . . R 10 42.306 -10.736 -31.523 1 45.62 ? S1 F3S 304 B 1 HETATM 5 S S2 F3S . . . R 10 39.613 -8.695 -29.73 1 49.39 ? S2 F3S 304 B 1 HETATM 6 S S3 F3S . . . R 10 39.25 -11.879 -30.671 1 45.26 ? S3 F3S 304 B 1 HETATM 7 S S4 F3S . . . R 10 41.677 -11.819 -28.087 1 46.15 ? S4 F3S 304 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 56 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 7 #