data_1KBP # _model_server_result.job_id uB7GLtN504Dap_BRM5hhsQ _model_server_result.datetime_utc '2024-12-01 00:03:46' _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 1kbp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":438}' # _entry.id 1KBP # _exptl.entry_id 1KBP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 55.845 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'FE (III) ION' _entity.pdbx_number_of_molecules 4 _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 1KBP _cell.length_a 132.7 _cell.length_b 347.3 _cell.length_c 128.7 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KBP _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression B,C,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,HA,IA 1 1,2 A,D,E,F,G,H,I,J,K,Z,AA,BA,CA,DA,EA,FA,GA,JA 2 1,3 # 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.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _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[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_556 x,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 128.7 3 'crystal symmetry operation' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 132.7 0 64.35 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 J N N ? 3 Q N N ? 3 X N N ? 3 EA 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 disulf ? disulf1 A SG CYS 345 A CYS 345 3_655 A SG CYS 345 A CYS 345 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? disulf ? disulf2 B SG CYS 345 B CYS 345 1_555 C SG CYS 345 C CYS 345 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? disulf ? disulf3 D SG CYS 345 D CYS 345 3_655 D SG CYS 345 D CYS 345 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? covale ? covale1 A ND2 ASN 81 A ASN 81 1_555 E C1 NAG . A NAG 433 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.474 ? covale ? covale2 A ND2 ASN 109 A ASN 109 1_555 F C1 NAG . A NAG 434 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.456 ? covale ? covale3 A ND2 ASN 143 A ASN 143 1_555 G C1 NAG . A NAG 435 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.456 ? covale ? covale4 A ND2 ASN 211 A ASN 211 1_555 H C1 NAG . A NAG 436 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.463 ? covale ? covale5 A ND2 ASN 396 A ASN 396 1_555 I C1 NAG . A NAG 437 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.474 ? covale ? covale6 B ND2 ASN 81 B ASN 81 1_555 L C1 NAG . B NAG 433 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.477 ? covale ? covale7 B ND2 ASN 109 B ASN 109 1_555 M C1 NAG . B NAG 434 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.465 ? covale ? covale8 B ND2 ASN 143 B ASN 143 1_555 N C1 NAG . B NAG 435 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.454 ? covale ? covale9 B ND2 ASN 211 B ASN 211 1_555 O C1 NAG . B NAG 436 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.465 ? covale ? covale10 B ND2 ASN 396 B ASN 396 1_555 P C1 NAG . B NAG 437 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.469 ? covale ? covale11 C ND2 ASN 81 C ASN 81 1_555 S C1 NAG . C NAG 433 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.476 ? covale ? covale12 C ND2 ASN 109 C ASN 109 1_555 T C1 NAG . C NAG 434 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.449 ? covale ? covale13 C ND2 ASN 143 C ASN 143 1_555 U C1 NAG . C NAG 435 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.445 ? covale ? covale14 C ND2 ASN 211 C ASN 211 1_555 V C1 NAG . C NAG 436 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.467 ? covale ? covale15 C ND2 ASN 396 C ASN 396 1_555 W C1 NAG . C NAG 437 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.468 ? covale ? covale16 D ND2 ASN 81 D ASN 81 1_555 Z C1 NAG . D NAG 433 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.471 ? covale ? covale17 D ND2 ASN 109 D ASN 109 1_555 AA C1 NAG . D NAG 434 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.455 ? covale ? covale18 D ND2 ASN 143 D ASN 143 1_555 BA C1 NAG . D NAG 435 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.462 ? covale ? covale19 D ND2 ASN 211 D ASN 211 1_555 CA C1 NAG . D NAG 436 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.466 ? covale ? covale20 D ND2 ASN 396 D ASN 396 1_555 DA C1 NAG . D NAG 437 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.47 ? metalc ? metalc1 A OD2 ASP 135 A ASP 135 1_555 J FE FE . A FE 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc2 A OD2 ASP 164 A ASP 164 1_555 J FE FE . A FE 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc3 A OD2 ASP 164 A ASP 164 1_555 K ZN ZN . A ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc4 A OH TYR 167 A TYR 167 1_555 J FE FE . A FE 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc5 A OD1 ASN 201 A ASN 201 1_555 K ZN ZN . A ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc6 A NE2 HIS 286 A HIS 286 1_555 K ZN ZN . A ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc7 A ND1 HIS 323 A HIS 323 1_555 K ZN ZN . A ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc8 A NE2 HIS 325 A HIS 325 1_555 J FE FE . A FE 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc9 B OD2 ASP 135 B ASP 135 1_555 Q FE FE . B FE 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc10 B OD2 ASP 164 B ASP 164 1_555 Q FE FE . B FE 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc11 B OD2 ASP 164 B ASP 164 1_555 R ZN ZN . B ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc12 B OH TYR 167 B TYR 167 1_555 Q FE FE . B FE 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc13 B OD1 ASN 201 B ASN 201 1_555 R ZN ZN . B ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc14 B NE2 HIS 286 B HIS 286 1_555 R ZN ZN . B ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc15 B ND1 HIS 323 B HIS 323 1_555 R ZN ZN . B ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc16 B NE2 HIS 325 B HIS 325 1_555 Q FE FE . B FE 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc17 C OD2 ASP 135 C ASP 135 1_555 X FE FE . C FE 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc18 C OD2 ASP 164 C ASP 164 1_555 X FE FE . C FE 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc19 C OD2 ASP 164 C ASP 164 1_555 Y ZN ZN . C ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc20 C OH TYR 167 C TYR 167 1_555 X FE FE . C FE 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc21 C OD1 ASN 201 C ASN 201 1_555 Y ZN ZN . C ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc22 C NE2 HIS 286 C HIS 286 1_555 Y ZN ZN . C ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc23 C ND1 HIS 323 C HIS 323 1_555 Y ZN ZN . C ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc24 C NE2 HIS 325 C HIS 325 1_555 X FE FE . C FE 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc25 D OD2 ASP 135 D ASP 135 1_555 EA FE FE . D FE 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? metalc ? metalc26 D OD2 ASP 164 D ASP 164 1_555 EA FE FE . D FE 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc27 D OD2 ASP 164 D ASP 164 1_555 FA ZN ZN . D ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc28 D OH TYR 167 D TYR 167 1_555 EA FE FE . D FE 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc29 D OD1 ASN 201 D ASN 201 1_555 FA ZN ZN . D ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc30 D NE2 HIS 286 D HIS 286 1_555 FA ZN ZN . D ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc31 D ND1 HIS 323 D HIS 323 1_555 FA ZN ZN . D ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc32 D NE2 HIS 325 D HIS 325 1_555 EA FE FE . D FE 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? # _chem_comp.formula 'Fe 3' _chem_comp.formula_weight 55.845 _chem_comp.id FE _chem_comp.mon_nstd_flag . _chem_comp.name 'FE (III) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1KBP _atom_sites.fract_transf_matrix[1][1] 0.007536 _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] 0.002879 _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] 0.00777 _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 E 2 NAG A 1 433 81 NAG NAG A F 2 NAG A 1 434 109 NAG NAG A G 2 NAG A 1 435 143 NAG NAG A H 2 NAG A 1 436 211 NAG NAG A I 2 NAG A 1 437 396 NAG NAG A J 3 FE A 1 438 433 FE FE . K 4 ZN A 1 439 434 ZN ZN . L 2 NAG B 1 433 81 NAG NAG A M 2 NAG B 1 434 109 NAG NAG A N 2 NAG B 1 435 143 NAG NAG A O 2 NAG B 1 436 211 NAG NAG A P 2 NAG B 1 437 396 NAG NAG A Q 3 FE B 1 438 433 FE FE . R 4 ZN B 1 439 434 ZN ZN . S 2 NAG C 1 433 81 NAG NAG A T 2 NAG C 1 434 109 NAG NAG A U 2 NAG C 1 435 143 NAG NAG A V 2 NAG C 1 436 211 NAG NAG A W 2 NAG C 1 437 396 NAG NAG A X 3 FE C 1 438 433 FE FE . Y 4 ZN C 1 439 434 ZN ZN . Z 2 NAG D 1 433 81 NAG NAG A AA 2 NAG D 1 434 109 NAG NAG A BA 2 NAG D 1 435 143 NAG NAG A CA 2 NAG D 1 436 211 NAG NAG A DA 2 NAG D 1 437 396 NAG NAG A EA 3 FE D 1 438 433 FE FE . FA 4 ZN D 1 439 434 ZN ZN . GA 5 HOH A 1 440 1 HOH HOH . GA 5 HOH A 2 441 2 HOH HOH . GA 5 HOH A 3 442 3 HOH HOH . GA 5 HOH A 4 443 4 HOH HOH . GA 5 HOH A 5 444 5 HOH HOH . GA 5 HOH A 6 445 6 HOH HOH . GA 5 HOH A 7 446 7 HOH HOH . GA 5 HOH A 8 447 8 HOH HOH . GA 5 HOH A 9 448 10 HOH HOH . GA 5 HOH A 10 449 11 HOH HOH . GA 5 HOH A 11 450 12 HOH HOH . GA 5 HOH A 12 451 13 HOH HOH . GA 5 HOH A 13 452 14 HOH HOH . GA 5 HOH A 14 453 15 HOH HOH . GA 5 HOH A 15 454 16 HOH HOH . GA 5 HOH A 16 455 17 HOH HOH . GA 5 HOH A 17 456 18 HOH HOH . GA 5 HOH A 18 457 63 HOH HOH . HA 5 HOH B 1 440 27 HOH HOH . HA 5 HOH B 2 441 19 HOH HOH . HA 5 HOH B 3 442 21 HOH HOH . HA 5 HOH B 4 443 22 HOH HOH . HA 5 HOH B 5 444 23 HOH HOH . HA 5 HOH B 6 445 24 HOH HOH . HA 5 HOH B 7 446 25 HOH HOH . HA 5 HOH B 8 447 26 HOH HOH . HA 5 HOH B 9 448 28 HOH HOH . HA 5 HOH B 10 449 29 HOH HOH . HA 5 HOH B 11 450 30 HOH HOH . HA 5 HOH B 12 451 32 HOH HOH . HA 5 HOH B 13 452 33 HOH HOH . HA 5 HOH B 14 453 34 HOH HOH . HA 5 HOH B 15 454 35 HOH HOH . HA 5 HOH B 16 455 36 HOH HOH . HA 5 HOH B 17 456 49 HOH HOH . IA 5 HOH C 1 440 45 HOH HOH . IA 5 HOH C 2 441 31 HOH HOH . IA 5 HOH C 3 442 37 HOH HOH . IA 5 HOH C 4 443 39 HOH HOH . IA 5 HOH C 5 444 40 HOH HOH . IA 5 HOH C 6 445 41 HOH HOH . IA 5 HOH C 7 446 42 HOH HOH . IA 5 HOH C 8 447 43 HOH HOH . IA 5 HOH C 9 448 44 HOH HOH . IA 5 HOH C 10 449 46 HOH HOH . IA 5 HOH C 11 450 47 HOH HOH . IA 5 HOH C 12 451 48 HOH HOH . IA 5 HOH C 13 452 50 HOH HOH . IA 5 HOH C 14 453 51 HOH HOH . IA 5 HOH C 15 454 52 HOH HOH . IA 5 HOH C 16 455 53 HOH HOH . IA 5 HOH C 17 456 54 HOH HOH . JA 5 HOH D 1 440 9 HOH HOH . JA 5 HOH D 2 441 55 HOH HOH . JA 5 HOH D 3 442 56 HOH HOH . JA 5 HOH D 4 443 57 HOH HOH . JA 5 HOH D 5 444 58 HOH HOH . JA 5 HOH D 6 445 59 HOH HOH . JA 5 HOH D 7 446 60 HOH HOH . JA 5 HOH D 8 447 61 HOH HOH . JA 5 HOH D 9 448 62 HOH HOH . JA 5 HOH D 10 449 64 HOH HOH . JA 5 HOH D 11 450 65 HOH HOH . JA 5 HOH D 12 451 66 HOH HOH . JA 5 HOH D 13 452 67 HOH HOH . JA 5 HOH D 14 453 68 HOH HOH . JA 5 HOH D 15 454 69 HOH HOH . JA 5 HOH D 16 455 70 HOH HOH . JA 5 HOH D 17 456 71 HOH HOH . JA 5 HOH D 18 457 72 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol FE _atom_site.label_atom_id FE _atom_site.label_comp_id FE _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id J _atom_site.label_entity_id 3 _atom_site.Cartn_x 67.934 _atom_site.Cartn_y 60.673 _atom_site.Cartn_z 51.581 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 33.83 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id FE _atom_site.auth_comp_id FE _atom_site.auth_seq_id 438 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #