data_5Z5O # _model_server_result.job_id Ki-4Ri9PTVZA23mqWxnYkA _model_server_result.datetime_utc '2024-10-10 23:35:07' _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 5z5o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 5Z5O # _exptl.entry_id 5Z5O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 8 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 91.83 _cell.angle_gamma 90 _cell.entry_id 5Z5O _cell.length_a 50.1 _cell.length_b 67.27 _cell.length_c 82.87 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Z5O _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,RA 1 1 B,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,SA 1 2 # 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_756 -x+2,y+1/2,-z+1 -1 0 0 0 1 0 0 0 -1 97.553622 33.635 82.827734 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N ? 3 E N N ? 3 F N N ? 3 G N N ? 3 H N N ? 3 I N N ? 3 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 disulf ? disulf1 A SG CYS 142 A CYS 121 1_555 A SG CYS 183 A CYS 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? disulf ? disulf2 A SG CYS 176 A CYS 155 1_555 A SG CYS 216 A CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf3 A SG CYS 275 A CYS 254 1_555 A SG CYS 324 A CYS 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? covale ? covale1 A C THR 88 A THR 67 1_555 A N SEB 89 A SEB 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale2 A C SEB 89 A SEB 68 1_555 A N GLU 90 A GLU 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? metalc ? metalc1 A OD2 ASP 175 A ASP 154 1_555 EA NA NA . A NA 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? metalc ? metalc2 A OE1 GLU 214 A GLU 193 1_555 EA NA NA . A NA 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc3 EA NA NA . A NA 429 1_555 RA O HOH . A HOH 522 2_756 ? ? ? ? ? ? ? ? ? ? ? ? 3.137 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 C1 O1 GOL sing 138 n n C1 C2 GOL sing 139 n n C1 H11 GOL sing 140 n n C1 H12 GOL sing 141 n n O1 HO1 GOL sing 142 n n C2 O2 GOL sing 143 n n C2 C3 GOL sing 144 n n C2 H2 GOL sing 145 n n O2 HO2 GOL sing 146 n n C3 O3 GOL sing 147 n n C3 H31 GOL sing 148 n n C3 H32 GOL sing 149 n n O3 HO3 GOL sing 150 n n # _atom_sites.entry_id 5Z5O _atom_sites.fract_transf_matrix[1][1] 0.01996 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000638 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014865 _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] 0.012073 _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 C 3 GOL A 1 401 315 GOL GOL . D 3 GOL A 1 402 316 GOL GOL . E 3 GOL A 1 403 317 GOL GOL . F 3 GOL A 1 404 318 GOL GOL . G 3 GOL A 1 405 319 GOL GOL . H 3 GOL A 1 406 320 GOL GOL . I 3 GOL A 1 407 321 GOL GOL . J 4 EDO A 1 408 322 EDO EDO . K 4 EDO A 1 409 323 EDO EDO . L 4 EDO A 1 410 324 EDO EDO . M 4 EDO A 1 411 325 EDO EDO . N 4 EDO A 1 412 326 EDO EDO . O 4 EDO A 1 413 327 EDO EDO . P 4 EDO A 1 414 328 EDO EDO . Q 4 EDO A 1 415 329 EDO EDO . R 4 EDO A 1 416 330 EDO EDO . S 4 EDO A 1 417 331 EDO EDO . T 4 EDO A 1 418 332 EDO EDO . U 4 EDO A 1 419 333 EDO EDO . V 4 EDO A 1 420 334 EDO EDO . W 5 SO4 A 1 421 335 SO4 SO4 . X 6 PEG A 1 422 336 PEG PEG . Y 6 PEG A 1 423 337 PEG PEG . Z 6 PEG A 1 424 338 PEG PEG . AA 6 PEG A 1 425 339 PEG PEG . BA 6 PEG A 1 426 340 PEG PEG . CA 6 PEG A 1 427 341 PEG PEG . DA 7 CL A 1 428 342 CL CL . EA 8 NA A 1 429 343 NA NA . FA 3 GOL B 1 101 74 GOL GOL . GA 4 EDO B 1 102 75 EDO EDO . HA 4 EDO B 1 103 76 EDO EDO . IA 4 EDO B 1 104 77 EDO EDO . JA 5 SO4 B 1 105 78 SO4 SO4 . KA 5 SO4 B 1 106 79 SO4 SO4 . LA 5 SO4 B 1 107 80 SO4 SO4 . MA 5 SO4 B 1 108 81 SO4 SO4 . NA 6 PEG B 1 109 82 PEG PEG . OA 9 MPD B 1 110 83 MPD MPD . PA 9 MPD B 1 111 84 MPD MPD . QA 9 MPD B 1 112 85 MPD MPD . RA 10 HOH A 1 501 493 HOH HOH . RA 10 HOH A 2 502 417 HOH HOH . RA 10 HOH A 3 503 392 HOH HOH . RA 10 HOH A 4 504 443 HOH HOH . RA 10 HOH A 5 505 365 HOH HOH . RA 10 HOH A 6 506 499 HOH HOH . RA 10 HOH A 7 507 518 HOH HOH . RA 10 HOH A 8 508 446 HOH HOH . RA 10 HOH A 9 509 457 HOH HOH . RA 10 HOH A 10 510 402 HOH HOH . RA 10 HOH A 11 511 442 HOH HOH . RA 10 HOH A 12 512 423 HOH HOH . RA 10 HOH A 13 513 497 HOH HOH . RA 10 HOH A 14 514 431 HOH HOH . RA 10 HOH A 15 515 517 HOH HOH . RA 10 HOH A 16 516 447 HOH HOH . RA 10 HOH A 17 517 483 HOH HOH . RA 10 HOH A 18 518 416 HOH HOH . RA 10 HOH A 19 519 449 HOH HOH . RA 10 HOH A 20 520 370 HOH HOH . RA 10 HOH A 21 521 397 HOH HOH . RA 10 HOH A 22 522 387 HOH HOH . RA 10 HOH A 23 523 393 HOH HOH . RA 10 HOH A 24 524 424 HOH HOH . RA 10 HOH A 25 525 519 HOH HOH . RA 10 HOH A 26 526 372 HOH HOH . RA 10 HOH A 27 527 357 HOH HOH . RA 10 HOH A 28 528 492 HOH HOH . RA 10 HOH A 29 529 349 HOH HOH . RA 10 HOH A 30 530 470 HOH HOH . RA 10 HOH A 31 531 501 HOH HOH . RA 10 HOH A 32 532 359 HOH HOH . RA 10 HOH A 33 533 502 HOH HOH . RA 10 HOH A 34 534 383 HOH HOH . RA 10 HOH A 35 535 469 HOH HOH . RA 10 HOH A 36 536 505 HOH HOH . RA 10 HOH A 37 537 490 HOH HOH . RA 10 HOH A 38 538 429 HOH HOH . RA 10 HOH A 39 539 347 HOH HOH . RA 10 HOH A 40 540 456 HOH HOH . RA 10 HOH A 41 541 363 HOH HOH . RA 10 HOH A 42 542 484 HOH HOH . RA 10 HOH A 43 543 360 HOH HOH . RA 10 HOH A 44 544 455 HOH HOH . RA 10 HOH A 45 545 375 HOH HOH . RA 10 HOH A 46 546 351 HOH HOH . RA 10 HOH A 47 547 386 HOH HOH . RA 10 HOH A 48 548 399 HOH HOH . RA 10 HOH A 49 549 488 HOH HOH . RA 10 HOH A 50 550 348 HOH HOH . RA 10 HOH A 51 551 461 HOH HOH . RA 10 HOH A 52 552 496 HOH HOH . RA 10 HOH A 53 553 504 HOH HOH . RA 10 HOH A 54 554 367 HOH HOH . RA 10 HOH A 55 555 421 HOH HOH . RA 10 HOH A 56 556 477 HOH HOH . RA 10 HOH A 57 557 407 HOH HOH . RA 10 HOH A 58 558 344 HOH HOH . RA 10 HOH A 59 559 369 HOH HOH . RA 10 HOH A 60 560 350 HOH HOH . RA 10 HOH A 61 561 450 HOH HOH . RA 10 HOH A 62 562 398 HOH HOH . RA 10 HOH A 63 563 394 HOH HOH . RA 10 HOH A 64 564 463 HOH HOH . RA 10 HOH A 65 565 400 HOH HOH . RA 10 HOH A 66 566 406 HOH HOH . RA 10 HOH A 67 567 454 HOH HOH . RA 10 HOH A 68 568 508 HOH HOH . RA 10 HOH A 69 569 376 HOH HOH . RA 10 HOH A 70 570 465 HOH HOH . RA 10 HOH A 71 571 354 HOH HOH . RA 10 HOH A 72 572 104 HOH HOH . RA 10 HOH A 73 573 427 HOH HOH . RA 10 HOH A 74 574 404 HOH HOH . RA 10 HOH A 75 575 509 HOH HOH . RA 10 HOH A 76 576 435 HOH HOH . RA 10 HOH A 77 577 368 HOH HOH . RA 10 HOH A 78 578 361 HOH HOH . RA 10 HOH A 79 579 353 HOH HOH . RA 10 HOH A 80 580 356 HOH HOH . RA 10 HOH A 81 581 345 HOH HOH . RA 10 HOH A 82 582 364 HOH HOH . RA 10 HOH A 83 583 346 HOH HOH . RA 10 HOH A 84 584 441 HOH HOH . RA 10 HOH A 85 585 444 HOH HOH . RA 10 HOH A 86 586 385 HOH HOH . RA 10 HOH A 87 587 436 HOH HOH . RA 10 HOH A 88 588 515 HOH HOH . RA 10 HOH A 89 589 413 HOH HOH . RA 10 HOH A 90 590 371 HOH HOH . RA 10 HOH A 91 591 366 HOH HOH . RA 10 HOH A 92 592 453 HOH HOH . RA 10 HOH A 93 593 381 HOH HOH . RA 10 HOH A 94 594 451 HOH HOH . RA 10 HOH A 95 595 377 HOH HOH . RA 10 HOH A 96 596 355 HOH HOH . RA 10 HOH A 97 597 498 HOH HOH . RA 10 HOH A 98 598 434 HOH HOH . RA 10 HOH A 99 599 480 HOH HOH . RA 10 HOH A 100 600 352 HOH HOH . RA 10 HOH A 101 601 362 HOH HOH . RA 10 HOH A 102 602 415 HOH HOH . RA 10 HOH A 103 603 388 HOH HOH . RA 10 HOH A 104 604 412 HOH HOH . RA 10 HOH A 105 605 396 HOH HOH . RA 10 HOH A 106 606 422 HOH HOH . RA 10 HOH A 107 607 358 HOH HOH . RA 10 HOH A 108 608 458 HOH HOH . RA 10 HOH A 109 609 440 HOH HOH . RA 10 HOH A 110 610 389 HOH HOH . RA 10 HOH A 111 611 410 HOH HOH . RA 10 HOH A 112 612 445 HOH HOH . RA 10 HOH A 113 613 382 HOH HOH . RA 10 HOH A 114 614 373 HOH HOH . RA 10 HOH A 115 615 403 HOH HOH . RA 10 HOH A 116 616 401 HOH HOH . RA 10 HOH A 117 617 391 HOH HOH . RA 10 HOH A 118 618 466 HOH HOH . RA 10 HOH A 119 619 378 HOH HOH . RA 10 HOH A 120 620 384 HOH HOH . RA 10 HOH A 121 621 506 HOH HOH . RA 10 HOH A 122 622 409 HOH HOH . RA 10 HOH A 123 623 420 HOH HOH . RA 10 HOH A 124 624 439 HOH HOH . RA 10 HOH A 125 625 491 HOH HOH . RA 10 HOH A 126 626 395 HOH HOH . RA 10 HOH A 127 627 473 HOH HOH . RA 10 HOH A 128 628 430 HOH HOH . RA 10 HOH A 129 629 472 HOH HOH . RA 10 HOH A 130 630 418 HOH HOH . RA 10 HOH A 131 631 428 HOH HOH . RA 10 HOH A 132 632 482 HOH HOH . RA 10 HOH A 133 633 438 HOH HOH . RA 10 HOH A 134 634 510 HOH HOH . RA 10 HOH A 135 635 464 HOH HOH . RA 10 HOH A 136 636 433 HOH HOH . RA 10 HOH A 137 637 485 HOH HOH . RA 10 HOH A 138 638 426 HOH HOH . RA 10 HOH A 139 639 516 HOH HOH . RA 10 HOH A 140 640 419 HOH HOH . RA 10 HOH A 141 641 390 HOH HOH . RA 10 HOH A 142 642 474 HOH HOH . RA 10 HOH A 143 643 380 HOH HOH . RA 10 HOH A 144 644 414 HOH HOH . RA 10 HOH A 145 645 460 HOH HOH . RA 10 HOH A 146 646 481 HOH HOH . RA 10 HOH A 147 647 425 HOH HOH . RA 10 HOH A 148 648 374 HOH HOH . RA 10 HOH A 149 649 503 HOH HOH . RA 10 HOH A 150 650 411 HOH HOH . RA 10 HOH A 151 651 462 HOH HOH . RA 10 HOH A 152 652 476 HOH HOH . RA 10 HOH A 153 653 379 HOH HOH . RA 10 HOH A 154 654 432 HOH HOH . RA 10 HOH A 155 655 437 HOH HOH . RA 10 HOH A 156 656 459 HOH HOH . RA 10 HOH A 157 657 452 HOH HOH . RA 10 HOH A 158 658 512 HOH HOH . RA 10 HOH A 159 659 489 HOH HOH . RA 10 HOH A 160 660 475 HOH HOH . RA 10 HOH A 161 661 479 HOH HOH . RA 10 HOH A 162 662 471 HOH HOH . RA 10 HOH A 163 663 467 HOH HOH . RA 10 HOH A 164 664 486 HOH HOH . RA 10 HOH A 165 665 405 HOH HOH . RA 10 HOH A 166 666 494 HOH HOH . RA 10 HOH A 167 667 478 HOH HOH . RA 10 HOH A 168 668 514 HOH HOH . RA 10 HOH A 169 669 487 HOH HOH . RA 10 HOH A 170 670 495 HOH HOH . RA 10 HOH A 171 671 468 HOH HOH . RA 10 HOH A 172 672 513 HOH HOH . RA 10 HOH A 173 673 448 HOH HOH . RA 10 HOH A 174 674 511 HOH HOH . RA 10 HOH A 175 675 500 HOH HOH . RA 10 HOH A 176 676 408 HOH HOH . RA 10 HOH A 177 677 507 HOH HOH . RA 10 HOH A 178 678 1 HOH HOH . SA 10 HOH B 1 201 110 HOH HOH . SA 10 HOH B 2 202 94 HOH HOH . SA 10 HOH B 3 203 96 HOH HOH . SA 10 HOH B 4 204 88 HOH HOH . SA 10 HOH B 5 205 100 HOH HOH . SA 10 HOH B 6 206 90 HOH HOH . SA 10 HOH B 7 207 89 HOH HOH . SA 10 HOH B 8 208 92 HOH HOH . SA 10 HOH B 9 209 91 HOH HOH . SA 10 HOH B 10 210 95 HOH HOH . SA 10 HOH B 11 211 93 HOH HOH . SA 10 HOH B 12 212 99 HOH HOH . SA 10 HOH B 13 213 103 HOH HOH . SA 10 HOH B 14 214 101 HOH HOH . SA 10 HOH B 15 215 106 HOH HOH . SA 10 HOH B 16 216 86 HOH HOH . SA 10 HOH B 17 217 102 HOH HOH . SA 10 HOH B 18 218 98 HOH HOH . SA 10 HOH B 19 219 107 HOH HOH . SA 10 HOH B 20 220 114 HOH HOH . SA 10 HOH B 21 221 97 HOH HOH . SA 10 HOH B 22 222 111 HOH HOH . SA 10 HOH B 23 223 105 HOH HOH . SA 10 HOH B 24 224 113 HOH HOH . SA 10 HOH B 25 225 108 HOH HOH . SA 10 HOH B 26 226 112 HOH HOH . SA 10 HOH B 27 227 87 HOH HOH . SA 10 HOH B 28 228 109 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 C C1 GOL . . . D 3 47.978 49.597 39.879 1 56.82 ? C1 GOL 402 A 1 HETATM 2 O O1 GOL . . . D 3 48.285 49.361 38.546 1 50.16 ? O1 GOL 402 A 1 HETATM 3 C C2 GOL . . . D 3 49.208 50.21 40.497 1 63.72 ? C2 GOL 402 A 1 HETATM 4 O O2 GOL . . . D 3 49.514 51.435 39.927 1 56.94 ? O2 GOL 402 A 1 HETATM 5 C C3 GOL . . . D 3 48.875 50.301 41.994 1 58.87 ? C3 GOL 402 A 1 HETATM 6 O O3 GOL . . . D 3 47.72 51.087 42.123 1 48.22 ? O3 GOL 402 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 6 #