data_6Y02 # _model_server_result.job_id pLHPnddbH9DQGGSLhM8j3w _model_server_result.datetime_utc '2024-11-26 22:00:35' _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 6y02 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":307}' # _entry.id 6Y02 # _exptl.entry_id 6Y02 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 78.133 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIMETHYL SULFOXIDE' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 100.51 _cell.angle_gamma 90 _cell.entry_id 6Y02 _cell.length_a 70.131 _cell.length_b 71.404 _cell.length_c 72.892 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Y02 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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,L,M,N,O _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 G N N ? 6 J 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 9 L CYS 1 1_555 B SG CYS 119 H CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? disulf ? disulf2 B SG CYS 28 H CYS 42 1_555 B SG CYS 44 H CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf3 B SG CYS 173 H CYS 168 1_555 B SG CYS 187 H CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf4 B SG CYS 201 H CYS 191 1_555 B SG CYS 231 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? covale ? covale1 B ND2 ASN 53 H ASN 60 1_555 K C1 NAG . H NAG 308 1_555 G ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 C C GLU 9 C GLU 525 1_555 C N TYS 10 C TYS 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 C C TYS 10 C TYS 526 1_555 C N LEU 11 C LEU 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? metalc ? metalc1 B O LYS 174 H LYS 169 1_555 D NA NA . H NA 301 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc2 B O LYS 174 H LYS 169 1_555 D NA NA . H NA 301 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc3 B O THR 177 H THR 172 1_555 D NA NA . H NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc4 B O PHE 215 H PHE 204 1_555 D NA NA . H NA 301 4_556 A ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc5 B O ARG 233 H ARG 221 1_555 E NA NA . H NA 302 1_555 A ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc6 B O LYS 236 H LYS 224 1_555 E NA NA . H NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc7 D NA NA . H NA 301 1_555 N O HOH . H HOH 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.893 ? metalc ? metalc8 D NA NA . H NA 301 1_555 N O HOH . H HOH 473 4_546 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc9 D NA NA . H NA 301 1_555 N O HOH . H HOH 546 4_546 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc10 E NA NA . H NA 302 1_555 N O HOH . H HOH 474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc11 E NA NA . H NA 302 1_555 N O HOH . H HOH 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? metalc ? metalc12 E NA NA . H NA 302 1_555 N O HOH . H HOH 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.821 ? metalc ? metalc13 E NA NA . H NA 302 1_555 N O HOH . H HOH 547 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? # _chem_comp.formula 'C2 H6 O S' _chem_comp.formula_weight 78.133 _chem_comp.id DMS _chem_comp.mon_nstd_flag . _chem_comp.name 'DIMETHYL SULFOXIDE' _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 S O DMS doub 83 n n S C1 DMS sing 84 n n S C2 DMS sing 85 n n C1 H11 DMS sing 86 n n C1 H12 DMS sing 87 n n C1 H13 DMS sing 88 n n C2 H21 DMS sing 89 n n C2 H22 DMS sing 90 n n C2 H23 DMS sing 91 n n # _atom_sites.entry_id 6Y02 _atom_sites.fract_transf_matrix[1][1] 0.014259 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002646 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014005 _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] 0.013953 _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 NA H 1 301 1 NA NA . E 4 NA H 1 302 2 NA NA . F 5 PO4 H 1 303 4 PO4 PO4 . G 6 DMS H 1 304 5 DMS DMS . H 7 GOL H 1 305 7 GOL GOL . I 8 O5Z H 1 306 1 O5Z 13K . J 6 DMS H 1 307 1 DMS DMS . K 9 NAG H 1 308 1 NAG NAG . L 7 GOL H 1 309 1 GOL GOL . M 10 HOH L 1 101 174 HOH HOH . M 10 HOH L 2 102 130 HOH HOH . M 10 HOH L 3 103 34 HOH HOH . M 10 HOH L 4 104 47 HOH HOH . M 10 HOH L 5 105 36 HOH HOH . M 10 HOH L 6 106 61 HOH HOH . M 10 HOH L 7 107 195 HOH HOH . M 10 HOH L 8 108 68 HOH HOH . M 10 HOH L 9 109 40 HOH HOH . M 10 HOH L 10 110 38 HOH HOH . M 10 HOH L 11 111 21 HOH HOH . M 10 HOH L 12 112 17 HOH HOH . M 10 HOH L 13 113 71 HOH HOH . M 10 HOH L 14 114 116 HOH HOH . M 10 HOH L 15 115 215 HOH HOH . M 10 HOH L 16 116 22 HOH HOH . M 10 HOH L 17 117 117 HOH HOH . M 10 HOH L 18 118 74 HOH HOH . M 10 HOH L 19 119 207 HOH HOH . M 10 HOH L 20 120 129 HOH HOH . M 10 HOH L 21 121 214 HOH HOH . M 10 HOH L 22 122 232 HOH HOH . M 10 HOH L 23 123 82 HOH HOH . M 10 HOH L 24 124 113 HOH HOH . M 10 HOH L 25 125 175 HOH HOH . N 10 HOH H 1 401 231 HOH HOH . N 10 HOH H 2 402 201 HOH HOH . N 10 HOH H 3 403 182 HOH HOH . N 10 HOH H 4 404 186 HOH HOH . N 10 HOH H 5 405 123 HOH HOH . N 10 HOH H 6 406 109 HOH HOH . N 10 HOH H 7 407 221 HOH HOH . N 10 HOH H 8 408 56 HOH HOH . N 10 HOH H 9 409 75 HOH HOH . N 10 HOH H 10 410 77 HOH HOH . N 10 HOH H 11 411 189 HOH HOH . N 10 HOH H 12 412 81 HOH HOH . N 10 HOH H 13 413 92 HOH HOH . N 10 HOH H 14 414 53 HOH HOH . N 10 HOH H 15 415 208 HOH HOH . N 10 HOH H 16 416 124 HOH HOH . N 10 HOH H 17 417 106 HOH HOH . N 10 HOH H 18 418 213 HOH HOH . N 10 HOH H 19 419 73 HOH HOH . N 10 HOH H 20 420 54 HOH HOH . N 10 HOH H 21 421 35 HOH HOH . N 10 HOH H 22 422 204 HOH HOH . N 10 HOH H 23 423 134 HOH HOH . N 10 HOH H 24 424 7 HOH HOH . N 10 HOH H 25 425 12 HOH HOH . N 10 HOH H 26 426 72 HOH HOH . N 10 HOH H 27 427 87 HOH HOH . N 10 HOH H 28 428 118 HOH HOH . N 10 HOH H 29 429 202 HOH HOH . N 10 HOH H 30 430 181 HOH HOH . N 10 HOH H 31 431 78 HOH HOH . N 10 HOH H 32 432 171 HOH HOH . N 10 HOH H 33 433 103 HOH HOH . N 10 HOH H 34 434 33 HOH HOH . N 10 HOH H 35 435 157 HOH HOH . N 10 HOH H 36 436 179 HOH HOH . N 10 HOH H 37 437 24 HOH HOH . N 10 HOH H 38 438 89 HOH HOH . N 10 HOH H 39 439 20 HOH HOH . N 10 HOH H 40 440 107 HOH HOH . N 10 HOH H 41 441 5 HOH HOH . N 10 HOH H 42 442 15 HOH HOH . N 10 HOH H 43 443 203 HOH HOH . N 10 HOH H 44 444 62 HOH HOH . N 10 HOH H 45 445 11 HOH HOH . N 10 HOH H 46 446 49 HOH HOH . N 10 HOH H 47 447 64 HOH HOH . N 10 HOH H 48 448 159 HOH HOH . N 10 HOH H 49 449 144 HOH HOH . N 10 HOH H 50 450 84 HOH HOH . N 10 HOH H 51 451 217 HOH HOH . N 10 HOH H 52 452 125 HOH HOH . N 10 HOH H 53 453 48 HOH HOH . N 10 HOH H 54 454 79 HOH HOH . N 10 HOH H 55 455 180 HOH HOH . N 10 HOH H 56 456 51 HOH HOH . N 10 HOH H 57 457 30 HOH HOH . N 10 HOH H 58 458 52 HOH HOH . N 10 HOH H 59 459 94 HOH HOH . N 10 HOH H 60 460 31 HOH HOH . N 10 HOH H 61 461 145 HOH HOH . N 10 HOH H 62 462 133 HOH HOH . N 10 HOH H 63 463 69 HOH HOH . N 10 HOH H 64 464 108 HOH HOH . N 10 HOH H 65 465 227 HOH HOH . N 10 HOH H 66 466 14 HOH HOH . N 10 HOH H 67 467 50 HOH HOH . N 10 HOH H 68 468 55 HOH HOH . N 10 HOH H 69 469 44 HOH HOH . N 10 HOH H 70 470 222 HOH HOH . N 10 HOH H 71 471 13 HOH HOH . N 10 HOH H 72 472 165 HOH HOH . N 10 HOH H 73 473 8 HOH HOH . N 10 HOH H 74 474 32 HOH HOH . N 10 HOH H 75 475 27 HOH HOH . N 10 HOH H 76 476 1 HOH HOH . N 10 HOH H 77 477 9 HOH HOH . N 10 HOH H 78 478 155 HOH HOH . N 10 HOH H 79 479 57 HOH HOH . N 10 HOH H 80 480 143 HOH HOH . N 10 HOH H 81 481 18 HOH HOH . N 10 HOH H 82 482 10 HOH HOH . N 10 HOH H 83 483 187 HOH HOH . N 10 HOH H 84 484 19 HOH HOH . N 10 HOH H 85 485 158 HOH HOH . N 10 HOH H 86 486 39 HOH HOH . N 10 HOH H 87 487 101 HOH HOH . N 10 HOH H 88 488 60 HOH HOH . N 10 HOH H 89 489 25 HOH HOH . N 10 HOH H 90 490 76 HOH HOH . N 10 HOH H 91 491 28 HOH HOH . N 10 HOH H 92 492 169 HOH HOH . N 10 HOH H 93 493 218 HOH HOH . N 10 HOH H 94 494 219 HOH HOH . N 10 HOH H 95 495 26 HOH HOH . N 10 HOH H 96 496 45 HOH HOH . N 10 HOH H 97 497 29 HOH HOH . N 10 HOH H 98 498 41 HOH HOH . N 10 HOH H 99 499 112 HOH HOH . N 10 HOH H 100 500 66 HOH HOH . N 10 HOH H 101 501 132 HOH HOH . N 10 HOH H 102 502 6 HOH HOH . N 10 HOH H 103 503 166 HOH HOH . N 10 HOH H 104 504 63 HOH HOH . N 10 HOH H 105 505 2 HOH HOH . N 10 HOH H 106 506 23 HOH HOH . N 10 HOH H 107 507 131 HOH HOH . N 10 HOH H 108 508 154 HOH HOH . N 10 HOH H 109 509 4 HOH HOH . N 10 HOH H 110 510 172 HOH HOH . N 10 HOH H 111 511 119 HOH HOH . N 10 HOH H 112 512 3 HOH HOH . N 10 HOH H 113 513 86 HOH HOH . N 10 HOH H 114 514 91 HOH HOH . N 10 HOH H 115 515 37 HOH HOH . N 10 HOH H 116 516 139 HOH HOH . N 10 HOH H 117 517 178 HOH HOH . N 10 HOH H 118 518 185 HOH HOH . N 10 HOH H 119 519 67 HOH HOH . N 10 HOH H 120 520 212 HOH HOH . N 10 HOH H 121 521 148 HOH HOH . N 10 HOH H 122 522 88 HOH HOH . N 10 HOH H 123 523 146 HOH HOH . N 10 HOH H 124 524 164 HOH HOH . N 10 HOH H 125 525 161 HOH HOH . N 10 HOH H 126 526 210 HOH HOH . N 10 HOH H 127 527 85 HOH HOH . N 10 HOH H 128 528 192 HOH HOH . N 10 HOH H 129 529 177 HOH HOH . N 10 HOH H 130 530 122 HOH HOH . N 10 HOH H 131 531 147 HOH HOH . N 10 HOH H 132 532 80 HOH HOH . N 10 HOH H 133 533 98 HOH HOH . N 10 HOH H 134 534 149 HOH HOH . N 10 HOH H 135 535 150 HOH HOH . N 10 HOH H 136 536 111 HOH HOH . N 10 HOH H 137 537 42 HOH HOH . N 10 HOH H 138 538 160 HOH HOH . N 10 HOH H 139 539 184 HOH HOH . N 10 HOH H 140 540 99 HOH HOH . N 10 HOH H 141 541 95 HOH HOH . N 10 HOH H 142 542 163 HOH HOH . N 10 HOH H 143 543 100 HOH HOH . N 10 HOH H 144 544 70 HOH HOH . N 10 HOH H 145 545 196 HOH HOH . N 10 HOH H 146 546 83 HOH HOH . N 10 HOH H 147 547 46 HOH HOH . N 10 HOH H 148 548 183 HOH HOH . N 10 HOH H 149 549 190 HOH HOH . N 10 HOH H 150 550 152 HOH HOH . N 10 HOH H 151 551 168 HOH HOH . N 10 HOH H 152 552 229 HOH HOH . N 10 HOH H 153 553 211 HOH HOH . N 10 HOH H 154 554 200 HOH HOH . N 10 HOH H 155 555 199 HOH HOH . N 10 HOH H 156 556 58 HOH HOH . N 10 HOH H 157 557 126 HOH HOH . N 10 HOH H 158 558 230 HOH HOH . N 10 HOH H 159 559 135 HOH HOH . N 10 HOH H 160 560 193 HOH HOH . N 10 HOH H 161 561 156 HOH HOH . N 10 HOH H 162 562 220 HOH HOH . N 10 HOH H 163 563 170 HOH HOH . N 10 HOH H 164 564 191 HOH HOH . N 10 HOH H 165 565 228 HOH HOH . N 10 HOH H 166 566 209 HOH HOH . N 10 HOH H 167 567 151 HOH HOH . N 10 HOH H 168 568 142 HOH HOH . N 10 HOH H 169 569 115 HOH HOH . N 10 HOH H 170 570 140 HOH HOH . N 10 HOH H 171 571 206 HOH HOH . N 10 HOH H 172 572 224 HOH HOH . N 10 HOH H 173 573 226 HOH HOH . N 10 HOH H 174 574 90 HOH HOH . N 10 HOH H 175 575 225 HOH HOH . N 10 HOH H 176 576 205 HOH HOH . N 10 HOH H 177 577 141 HOH HOH . O 10 HOH C 1 601 198 HOH HOH . O 10 HOH C 2 602 176 HOH HOH . O 10 HOH C 3 603 188 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 S S DMS . . . J 6 16.684 -24.909 32.713 1 56.25 ? S DMS 307 H 1 HETATM 2 O O DMS . . . J 6 17.227 -23.516 32.723 1 54.2 ? O DMS 307 H 1 HETATM 3 C C1 DMS . . . J 6 14.877 -24.869 32.863 1 56.31 ? C1 DMS 307 H 1 HETATM 4 C C2 DMS . . . J 6 16.835 -25.567 31.025 1 57.2 ? C2 DMS 307 H 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 4 #