data_4YLF # _model_server_result.job_id Jb1JX-IYZEvdh7wjzg1x6Q _model_server_result.datetime_utc '2024-11-09 01:31:40' _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 4ylf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":501}' # _entry.id 4YLF # _exptl.entry_id 4YLF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 351.64 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'IRON/SULFUR CLUSTER' _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 4YLF _cell.length_a 81.42 _cell.length_b 81.42 _cell.length_c 311.48 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YLF _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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 A,B,E,F,G,H,I,J,Q,R 1 1 C,D,K,L,M,N,O,P,S,T 2 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 ? 5 G N N ? 5 H N N ? 5 M N N ? 5 N 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 metalc ? metalc1 A OD1 ASP 220 A ASP 220 1_555 E FE2 FES . A FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc2 A OD2 ASP 220 A ASP 220 1_555 E FE2 FES . A FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc3 A SG CYS 225 A CYS 225 1_555 E FE2 FES . A FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc4 A SG CYS 228 A CYS 228 1_555 E FE1 FES . A FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc5 A SG CYS 240 A CYS 240 1_555 E FE1 FES . A FES 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc6 B SG CYS 39 B CYS 39 1_555 G FE4 SF4 . B SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc7 B SG CYS 42 B CYS 42 1_555 G FE3 SF4 . B SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc8 B SG CYS 47 B CYS 47 1_555 G FE2 SF4 . B SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc9 B SG CYS 51 B CYS 51 1_555 H FE4 SF4 . B SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc10 B SG CYS 90 B CYS 90 1_555 H FE2 SF4 . B SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc11 B SG CYS 96 B CYS 96 1_555 H FE3 SF4 . B SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc12 B SG CYS 100 B CYS 100 1_555 G FE1 SF4 . B SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc13 B OE1 GLU 117 B GLU 117 1_555 H FE1 SF4 . B SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.826 ? metalc ? metalc14 C OD1 ASP 220 C ASP 220 1_555 L FE2 FES . C FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc15 C SG CYS 225 C CYS 225 1_555 L FE2 FES . C FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc16 C SG CYS 228 C CYS 228 1_555 L FE1 FES . C FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc17 C SG CYS 240 C CYS 240 1_555 L FE1 FES . C FES 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc18 D SG CYS 39 D CYS 39 1_555 M FE4 SF4 . D SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc19 D SG CYS 42 D CYS 42 1_555 M FE1 SF4 . D SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc20 D SG CYS 47 D CYS 47 1_555 M FE2 SF4 . D SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc21 D SG CYS 51 D CYS 51 1_555 N FE4 SF4 . D SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc22 D SG CYS 90 D CYS 90 1_555 N FE1 SF4 . D SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc23 D SG CYS 96 D CYS 96 1_555 N FE3 SF4 . D SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc24 D SG CYS 100 D CYS 100 1_555 M FE3 SF4 . D SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc25 D OE1 GLU 117 D GLU 117 1_555 N FE2 SF4 . D SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.816 ? # _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 389 n n FE1 S3 SF4 sing 390 n n FE1 S4 SF4 sing 391 n n FE2 S1 SF4 sing 392 n n FE2 S3 SF4 sing 393 n n FE2 S4 SF4 sing 394 n n FE3 S1 SF4 sing 395 n n FE3 S2 SF4 sing 396 n n FE3 S4 SF4 sing 397 n n FE4 S1 SF4 sing 398 n n FE4 S2 SF4 sing 399 n n FE4 S3 SF4 sing 400 n n # _atom_sites.entry_id 4YLF _atom_sites.fract_transf_matrix[1][1] 0.012282 _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] 0.012282 _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] 0.00321 _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 3 FES A 1 501 501 FES FES . F 4 FAD A 1 502 502 FAD FAD . G 5 SF4 B 1 501 501 SF4 SF4 . H 5 SF4 B 1 502 502 SF4 SF4 . I 4 FAD B 1 503 503 FAD FAD . J 6 PO4 B 1 504 1 PO4 PO4 . K 4 FAD C 1 301 666 FAD FAD . L 3 FES C 1 302 665 FES FES . M 5 SF4 D 1 501 999 SF4 SF4 . N 5 SF4 D 1 502 998 SF4 SF4 . O 4 FAD D 1 503 667 FAD FAD . P 6 PO4 D 1 504 1 PO4 PO4 . Q 7 HOH A 1 601 288 HOH HOH . Q 7 HOH A 2 602 147 HOH HOH . Q 7 HOH A 3 603 315 HOH HOH . Q 7 HOH A 4 604 90 HOH HOH . Q 7 HOH A 5 605 57 HOH HOH . Q 7 HOH A 6 606 437 HOH HOH . Q 7 HOH A 7 607 115 HOH HOH . Q 7 HOH A 8 608 190 HOH HOH . Q 7 HOH A 9 609 72 HOH HOH . Q 7 HOH A 10 610 425 HOH HOH . Q 7 HOH A 11 611 424 HOH HOH . Q 7 HOH A 12 612 187 HOH HOH . Q 7 HOH A 13 613 228 HOH HOH . Q 7 HOH A 14 614 259 HOH HOH . Q 7 HOH A 15 615 148 HOH HOH . Q 7 HOH A 16 616 274 HOH HOH . Q 7 HOH A 17 617 196 HOH HOH . Q 7 HOH A 18 618 63 HOH HOH . Q 7 HOH A 19 619 272 HOH HOH . Q 7 HOH A 20 620 284 HOH HOH . Q 7 HOH A 21 621 264 HOH HOH . R 7 HOH B 1 601 410 HOH HOH . R 7 HOH B 2 602 41 HOH HOH . R 7 HOH B 3 603 103 HOH HOH . R 7 HOH B 4 604 131 HOH HOH . R 7 HOH B 5 605 175 HOH HOH . R 7 HOH B 6 606 185 HOH HOH . R 7 HOH B 7 607 401 HOH HOH . R 7 HOH B 8 608 104 HOH HOH . R 7 HOH B 9 609 262 HOH HOH . R 7 HOH B 10 610 53 HOH HOH . R 7 HOH B 11 611 87 HOH HOH . R 7 HOH B 12 612 16 HOH HOH . R 7 HOH B 13 613 4 HOH HOH . R 7 HOH B 14 614 226 HOH HOH . R 7 HOH B 15 615 101 HOH HOH . R 7 HOH B 16 616 54 HOH HOH . R 7 HOH B 17 617 166 HOH HOH . R 7 HOH B 18 618 46 HOH HOH . R 7 HOH B 19 619 23 HOH HOH . R 7 HOH B 20 620 74 HOH HOH . R 7 HOH B 21 621 426 HOH HOH . R 7 HOH B 22 622 111 HOH HOH . R 7 HOH B 23 623 92 HOH HOH . R 7 HOH B 24 624 34 HOH HOH . R 7 HOH B 25 625 109 HOH HOH . R 7 HOH B 26 626 10 HOH HOH . R 7 HOH B 27 627 138 HOH HOH . R 7 HOH B 28 628 189 HOH HOH . R 7 HOH B 29 629 58 HOH HOH . R 7 HOH B 30 630 78 HOH HOH . R 7 HOH B 31 631 422 HOH HOH . R 7 HOH B 32 632 430 HOH HOH . R 7 HOH B 33 633 398 HOH HOH . R 7 HOH B 34 634 237 HOH HOH . R 7 HOH B 35 635 143 HOH HOH . R 7 HOH B 36 636 402 HOH HOH . R 7 HOH B 37 637 126 HOH HOH . R 7 HOH B 38 638 362 HOH HOH . R 7 HOH B 39 639 344 HOH HOH . R 7 HOH B 40 640 257 HOH HOH . R 7 HOH B 41 641 428 HOH HOH . R 7 HOH B 42 642 439 HOH HOH . R 7 HOH B 43 643 399 HOH HOH . R 7 HOH B 44 644 21 HOH HOH . R 7 HOH B 45 645 395 HOH HOH . R 7 HOH B 46 646 113 HOH HOH . R 7 HOH B 47 647 225 HOH HOH . R 7 HOH B 48 648 305 HOH HOH . R 7 HOH B 49 649 394 HOH HOH . R 7 HOH B 50 650 168 HOH HOH . R 7 HOH B 51 651 243 HOH HOH . R 7 HOH B 52 652 202 HOH HOH . R 7 HOH B 53 653 152 HOH HOH . R 7 HOH B 54 654 434 HOH HOH . R 7 HOH B 55 655 338 HOH HOH . R 7 HOH B 56 656 80 HOH HOH . R 7 HOH B 57 657 342 HOH HOH . R 7 HOH B 58 658 260 HOH HOH . S 7 HOH C 1 401 82 HOH HOH . S 7 HOH C 2 402 183 HOH HOH . S 7 HOH C 3 403 112 HOH HOH . S 7 HOH C 4 404 416 HOH HOH . S 7 HOH C 5 405 184 HOH HOH . S 7 HOH C 6 406 265 HOH HOH . S 7 HOH C 7 407 121 HOH HOH . S 7 HOH C 8 408 419 HOH HOH . S 7 HOH C 9 409 314 HOH HOH . S 7 HOH C 10 410 363 HOH HOH . S 7 HOH C 11 411 417 HOH HOH . S 7 HOH C 12 412 316 HOH HOH . S 7 HOH C 13 413 280 HOH HOH . S 7 HOH C 14 414 244 HOH HOH . S 7 HOH C 15 415 258 HOH HOH . S 7 HOH C 16 416 224 HOH HOH . S 7 HOH C 17 417 133 HOH HOH . S 7 HOH C 18 418 349 HOH HOH . T 7 HOH D 1 601 414 HOH HOH . T 7 HOH D 2 602 227 HOH HOH . T 7 HOH D 3 603 436 HOH HOH . T 7 HOH D 4 604 435 HOH HOH . T 7 HOH D 5 605 397 HOH HOH . T 7 HOH D 6 606 429 HOH HOH . T 7 HOH D 7 607 45 HOH HOH . T 7 HOH D 8 608 407 HOH HOH . T 7 HOH D 9 609 25 HOH HOH . T 7 HOH D 10 610 210 HOH HOH . T 7 HOH D 11 611 427 HOH HOH . T 7 HOH D 12 612 421 HOH HOH . T 7 HOH D 13 613 88 HOH HOH . T 7 HOH D 14 614 423 HOH HOH . T 7 HOH D 15 615 440 HOH HOH . T 7 HOH D 16 616 403 HOH HOH . T 7 HOH D 17 617 124 HOH HOH . T 7 HOH D 18 618 418 HOH HOH . T 7 HOH D 19 619 441 HOH HOH . T 7 HOH D 20 620 33 HOH HOH . T 7 HOH D 21 621 164 HOH HOH . T 7 HOH D 22 622 59 HOH HOH . T 7 HOH D 23 623 318 HOH HOH . T 7 HOH D 24 624 6 HOH HOH . T 7 HOH D 25 625 214 HOH HOH . T 7 HOH D 26 626 404 HOH HOH . T 7 HOH D 27 627 61 HOH HOH . T 7 HOH D 28 628 267 HOH HOH . T 7 HOH D 29 629 304 HOH HOH . T 7 HOH D 30 630 413 HOH HOH . T 7 HOH D 31 631 233 HOH HOH . T 7 HOH D 32 632 161 HOH HOH . T 7 HOH D 33 633 254 HOH HOH . T 7 HOH D 34 634 442 HOH HOH . T 7 HOH D 35 635 98 HOH HOH . T 7 HOH D 36 636 415 HOH HOH . T 7 HOH D 37 637 232 HOH HOH . T 7 HOH D 38 638 22 HOH HOH . T 7 HOH D 39 639 333 HOH HOH . T 7 HOH D 40 640 411 HOH HOH . T 7 HOH D 41 641 31 HOH HOH . T 7 HOH D 42 642 91 HOH HOH . T 7 HOH D 43 643 405 HOH HOH . T 7 HOH D 44 644 156 HOH HOH . T 7 HOH D 45 645 64 HOH HOH . T 7 HOH D 46 646 52 HOH HOH . T 7 HOH D 47 647 329 HOH HOH . T 7 HOH D 48 648 431 HOH HOH . T 7 HOH D 49 649 433 HOH HOH . T 7 HOH D 50 650 392 HOH HOH . T 7 HOH D 51 651 68 HOH HOH . T 7 HOH D 52 652 438 HOH HOH . T 7 HOH D 53 653 319 HOH HOH . T 7 HOH D 54 654 67 HOH HOH . T 7 HOH D 55 655 432 HOH HOH . T 7 HOH D 56 656 142 HOH HOH . T 7 HOH D 57 657 17 HOH HOH . T 7 HOH D 58 658 242 HOH HOH . T 7 HOH D 59 659 151 HOH HOH . T 7 HOH D 60 660 153 HOH HOH . T 7 HOH D 61 661 299 HOH HOH . T 7 HOH D 62 662 51 HOH HOH . T 7 HOH D 63 663 321 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 . . . G 5 -45.091 19.927 -10.531 1 162.48 ? FE1 SF4 501 B 1 HETATM 2 FE FE2 SF4 . . . G 5 -47.018 19.456 -8.285 1 256.69 ? FE2 SF4 501 B 1 HETATM 3 FE FE3 SF4 . . . G 5 -48.09 19.302 -11.233 1 30.17 ? FE3 SF4 501 B 1 HETATM 4 FE FE4 SF4 . . . G 5 -47.376 21.985 -10.06 1 33.11 ? FE4 SF4 501 B 1 HETATM 5 S S1 SF4 . . . G 5 -48.648 20.358 -9.396 1 42.32 ? S1 SF4 501 B 1 HETATM 6 S S2 SF4 . . . G 5 -46.632 20.841 -11.767 1 39.57 ? S2 SF4 501 B 1 HETATM 7 S S3 SF4 . . . G 5 -45.768 21.138 -8.849 1 83.13 ? S3 SF4 501 B 1 HETATM 8 S S4 SF4 . . . G 5 -46.506 18.336 -10.077 1 86.66 ? S4 SF4 501 B 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 8 #