data_1NEK # _model_server_result.job_id JQPbR8wR-USMSzXCnmyx-A _model_server_result.datetime_utc '2024-11-06 01:56:40' _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 1nek # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":304}' # _entry.id 1NEK # _exptl.entry_id 1NEK _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 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 120 _cell.entry_id 1NEK _cell.length_a 138.8 _cell.length_b 138.8 _cell.length_c 521.9 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NEK _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # 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 dodecameric 12 software_defined_assembly 2 PISA octameric 8 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,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S 2 1,2,3 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S 3 1,4 # 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' 2_765 -y+2,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 208.2 120.204326 0 3 'crystal symmetry operation' 3_675 -x+y+1,-x+2,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 240.408652 0 4 'crystal symmetry operation' 11_565 x-y+2/3,-y+4/3,-z+1/3 1 0 0 0 -1 0 0 0 -1 0 160.272435 173.966667 # _struct_asym.details ? _struct_asym.entity_id 10 _struct_asym.id K _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 metalc ? metalc1 I FE1 FES . B FES 302 1_555 B SG CYS 75 B CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc2 I FE1 FES . B FES 302 1_555 B OD1 ASP 63 B ASP 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc3 I FE1 FES . B FES 302 1_555 B OD2 ASP 63 B ASP 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc4 I FE2 FES . B FES 302 1_555 B SG CYS 60 B CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc5 I FE2 FES . B FES 302 1_555 B SG CYS 55 B CYS 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc6 J FE1 SF4 . B SF4 303 1_555 B SG CYS 155 B CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc7 J FE2 SF4 . B SF4 303 1_555 B SG CYS 149 B CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc8 J FE3 SF4 . B SF4 303 1_555 B SG CYS 216 B CYS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc9 J FE4 SF4 . B SF4 303 1_555 B SG CYS 152 B CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc10 K FE1 F3S . B F3S 304 1_555 B SG CYS 206 B CYS 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc11 K FE3 F3S . B F3S 304 1_555 B SG CYS 212 B CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc12 K FE4 F3S . B F3S 304 1_555 B SG CYS 159 B CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? covale ? covale1 A NE2 HIS 45 A HIS 45 1_555 G C8M FAD . A FAD 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? metalc ? metalc13 L FE HEM . C HEM 305 1_555 C NE2 HIS 84 C HIS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc14 L FE HEM . C HEM 305 1_555 D NE2 HIS 71 D HIS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc15 A O MET 356 A MET 356 1_555 F CA CA . A CA 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.01 ? metalc ? metalc16 A O MET 357 A MET 357 1_555 F CA CA . A CA 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? metalc ? metalc17 A O GLU 388 A GLU 388 1_555 F CA CA . A CA 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.989 ? metalc ? metalc18 A O ALA 390 A ALA 390 1_555 F CA CA . A CA 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.889 ? metalc ? metalc19 B O ASP 187 B ASP 187 1_555 H CA CA . B CA 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.987 ? metalc ? metalc20 B OG1 THR 190 B THR 190 1_555 H CA CA . B CA 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? # _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 ? # _atom_sites.entry_id 1NEK _atom_sites.fract_transf_matrix[1][1] 0.007205 _atom_sites.fract_transf_matrix[1][2] 0.00416 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008319 _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] 0.001916 _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 5 OAA A 1 589 7 OAA OAA . F 6 CA A 1 590 10 CA CA . G 7 FAD A 1 601 1 FAD FAD . H 6 CA B 1 311 11 CA CA . I 8 FES B 1 302 2 FES FES . J 9 SF4 B 1 303 3 SF4 FS4 . K 10 F3S B 1 304 4 F3S F3S . L 11 HEM C 1 305 5 HEM HEM . M 12 CDN C 1 308 8 CDN CL2 . N 13 EPH C 1 309 9 EPH EPH . O 14 UQ2 D 1 306 6 UQ2 UQ2 . P 15 HOH A 1 602 2 HOH HOH . P 15 HOH A 2 603 3 HOH HOH . P 15 HOH A 3 604 4 HOH HOH . P 15 HOH A 4 605 5 HOH HOH . P 15 HOH A 5 606 7 HOH HOH . P 15 HOH A 6 607 8 HOH HOH . P 15 HOH A 7 608 13 HOH HOH . P 15 HOH A 8 609 14 HOH HOH . P 15 HOH A 9 610 16 HOH HOH . P 15 HOH A 10 611 17 HOH HOH . P 15 HOH A 11 612 19 HOH HOH . P 15 HOH A 12 613 20 HOH HOH . P 15 HOH A 13 614 23 HOH HOH . P 15 HOH A 14 615 25 HOH HOH . P 15 HOH A 15 616 30 HOH HOH . P 15 HOH A 16 617 31 HOH HOH . P 15 HOH A 17 618 34 HOH HOH . P 15 HOH A 18 619 35 HOH HOH . P 15 HOH A 19 620 37 HOH HOH . P 15 HOH A 20 621 46 HOH HOH . P 15 HOH A 21 622 47 HOH HOH . P 15 HOH A 22 623 48 HOH HOH . P 15 HOH A 23 624 52 HOH HOH . P 15 HOH A 24 625 56 HOH HOH . P 15 HOH A 25 626 59 HOH HOH . P 15 HOH A 26 627 60 HOH HOH . P 15 HOH A 27 628 61 HOH HOH . P 15 HOH A 28 629 64 HOH HOH . P 15 HOH A 29 630 72 HOH HOH . P 15 HOH A 30 631 73 HOH HOH . P 15 HOH A 31 632 74 HOH HOH . P 15 HOH A 32 633 79 HOH HOH . P 15 HOH A 33 634 80 HOH HOH . P 15 HOH A 34 635 81 HOH HOH . P 15 HOH A 35 636 82 HOH HOH . P 15 HOH A 36 637 83 HOH HOH . P 15 HOH A 37 638 84 HOH HOH . P 15 HOH A 38 639 86 HOH HOH . P 15 HOH A 39 640 91 HOH HOH . P 15 HOH A 40 641 93 HOH HOH . P 15 HOH A 41 642 96 HOH HOH . P 15 HOH A 42 643 97 HOH HOH . P 15 HOH A 43 644 98 HOH HOH . P 15 HOH A 44 645 101 HOH HOH . P 15 HOH A 45 646 103 HOH HOH . P 15 HOH A 46 647 104 HOH HOH . P 15 HOH A 47 648 105 HOH HOH . P 15 HOH A 48 649 109 HOH HOH . P 15 HOH A 49 650 111 HOH HOH . P 15 HOH A 50 651 112 HOH HOH . P 15 HOH A 51 652 117 HOH HOH . P 15 HOH A 52 653 118 HOH HOH . P 15 HOH A 53 654 119 HOH HOH . P 15 HOH A 54 655 121 HOH HOH . P 15 HOH A 55 656 126 HOH HOH . P 15 HOH A 56 657 127 HOH HOH . P 15 HOH A 57 658 130 HOH HOH . P 15 HOH A 58 659 134 HOH HOH . P 15 HOH A 59 660 137 HOH HOH . P 15 HOH A 60 661 138 HOH HOH . P 15 HOH A 61 662 139 HOH HOH . Q 15 HOH B 1 312 6 HOH HOH . Q 15 HOH B 2 313 9 HOH HOH . Q 15 HOH B 3 314 10 HOH HOH . Q 15 HOH B 4 315 15 HOH HOH . Q 15 HOH B 5 316 18 HOH HOH . Q 15 HOH B 6 317 21 HOH HOH . Q 15 HOH B 7 318 22 HOH HOH . Q 15 HOH B 8 319 24 HOH HOH . Q 15 HOH B 9 320 27 HOH HOH . Q 15 HOH B 10 321 29 HOH HOH . Q 15 HOH B 11 322 32 HOH HOH . Q 15 HOH B 12 323 36 HOH HOH . Q 15 HOH B 13 324 38 HOH HOH . Q 15 HOH B 14 325 41 HOH HOH . Q 15 HOH B 15 326 43 HOH HOH . Q 15 HOH B 16 327 50 HOH HOH . Q 15 HOH B 17 328 51 HOH HOH . Q 15 HOH B 18 329 55 HOH HOH . Q 15 HOH B 19 330 57 HOH HOH . Q 15 HOH B 20 331 62 HOH HOH . Q 15 HOH B 21 332 65 HOH HOH . Q 15 HOH B 22 333 66 HOH HOH . Q 15 HOH B 23 334 69 HOH HOH . Q 15 HOH B 24 335 71 HOH HOH . Q 15 HOH B 25 336 75 HOH HOH . Q 15 HOH B 26 337 76 HOH HOH . Q 15 HOH B 27 338 77 HOH HOH . Q 15 HOH B 28 339 78 HOH HOH . Q 15 HOH B 29 340 85 HOH HOH . Q 15 HOH B 30 341 87 HOH HOH . Q 15 HOH B 31 342 88 HOH HOH . Q 15 HOH B 32 343 89 HOH HOH . Q 15 HOH B 33 344 90 HOH HOH . Q 15 HOH B 34 345 92 HOH HOH . Q 15 HOH B 35 346 94 HOH HOH . Q 15 HOH B 36 347 99 HOH HOH . Q 15 HOH B 37 348 100 HOH HOH . Q 15 HOH B 38 349 102 HOH HOH . Q 15 HOH B 39 350 114 HOH HOH . Q 15 HOH B 40 351 115 HOH HOH . Q 15 HOH B 41 352 116 HOH HOH . Q 15 HOH B 42 353 122 HOH HOH . Q 15 HOH B 43 354 123 HOH HOH . Q 15 HOH B 44 355 124 HOH HOH . Q 15 HOH B 45 356 125 HOH HOH . Q 15 HOH B 46 357 128 HOH HOH . Q 15 HOH B 47 358 129 HOH HOH . Q 15 HOH B 48 359 132 HOH HOH . Q 15 HOH B 49 360 133 HOH HOH . Q 15 HOH B 50 361 135 HOH HOH . R 15 HOH C 1 310 1 HOH HOH . R 15 HOH C 2 311 26 HOH HOH . R 15 HOH C 3 312 28 HOH HOH . R 15 HOH C 4 313 40 HOH HOH . R 15 HOH C 5 314 44 HOH HOH . R 15 HOH C 6 315 49 HOH HOH . R 15 HOH C 7 316 54 HOH HOH . R 15 HOH C 8 317 58 HOH HOH . R 15 HOH C 9 318 95 HOH HOH . R 15 HOH C 10 319 106 HOH HOH . R 15 HOH C 11 320 107 HOH HOH . R 15 HOH C 12 321 113 HOH HOH . R 15 HOH C 13 322 120 HOH HOH . R 15 HOH C 14 323 131 HOH HOH . R 15 HOH C 15 324 136 HOH HOH . S 15 HOH D 1 307 11 HOH HOH . S 15 HOH D 2 308 12 HOH HOH . S 15 HOH D 3 309 33 HOH HOH . S 15 HOH D 4 310 39 HOH HOH . S 15 HOH D 5 311 42 HOH HOH . S 15 HOH D 6 312 45 HOH HOH . S 15 HOH D 7 313 53 HOH HOH . S 15 HOH D 8 314 63 HOH HOH . S 15 HOH D 9 315 67 HOH HOH . S 15 HOH D 10 316 68 HOH HOH . S 15 HOH D 11 317 70 HOH HOH . S 15 HOH D 12 318 108 HOH HOH . S 15 HOH D 13 319 110 HOH HOH . S 15 HOH D 14 320 140 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 F3S . . . K 10 76.653 95.586 113.211 1 22.28 ? FE1 F3S 304 B 1 HETATM 2 FE FE3 F3S . . . K 10 77.388 93.408 114.625 1 21.01 ? FE3 F3S 304 B 1 HETATM 3 FE FE4 F3S . . . K 10 79.264 95.393 114.073 1 23.35 ? FE4 F3S 304 B 1 HETATM 4 S S1 F3S . . . K 10 76.057 93.477 112.805 1 16.1 ? S1 F3S 304 B 1 HETATM 5 S S2 F3S . . . K 10 78.576 96.085 112.003 1 14.28 ? S2 F3S 304 B 1 HETATM 6 S S3 F3S . . . K 10 77.389 95.593 115.416 1 29.22 ? S3 F3S 304 B 1 HETATM 7 S S4 F3S . . . K 10 79.529 93.201 113.886 1 23.54 ? S4 F3S 304 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 7 #