data_6YKD
#
_model_server_result.job_id            ApcZHrWb4-vLBPoKq88wOg 
_model_server_result.datetime_utc      '2025-01-19 20:42:06' 
_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          6ykd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":402}' 
#
_entry.id    6YKD 
#
_exptl.entry_id    6YKD 
_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    2 
_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            6YKD 
_cell.length_a            98.645 
_cell.length_b            98.645 
_cell.length_c            80.699 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YKD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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
? 3 C N N 
? 3 D 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
covale ? covale1 A C SER 276 A SER 260 1_555 A N SEP 277 A SEP 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale2 A C SEP 277 A SEP 261 1_555 A N GLU 278 A GLU 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
#
_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 135 n n 
C1 C2 GOL sing 136 n n 
C1 H11 GOL sing 137 n n 
C1 H12 GOL sing 138 n n 
O1 HO1 GOL sing 139 n n 
C2 O2 GOL sing 140 n n 
C2 C3 GOL sing 141 n n 
C2 H2 GOL sing 142 n n 
O2 HO2 GOL sing 143 n n 
C3 O3 GOL sing 144 n n 
C3 H31 GOL sing 145 n n 
C3 H32 GOL sing 146 n n 
O3 HO3 GOL sing 147 n n 
#
_atom_sites.entry_id                     6YKD 
_atom_sites.fract_transf_matrix[1][1]    0.010137 
_atom_sites.fract_transf_matrix[1][2]    0.005853 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011706 
_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]    0.012392 
_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
B 2 OWB A 1 400 400 OWB PM1 . 
C 3 GOL A 1 401 401 GOL GOL . 
D 3 GOL A 1 402 402 GOL GOL . 
E 4 ACT A 1 403 403 ACT ACT . 
F 5 HOH A 1 501 509 HOH HOH . 
F 5 HOH A 2 502 546 HOH HOH . 
F 5 HOH A 3 503 399 HOH HOH . 
F 5 HOH A 4 504 495 HOH HOH . 
F 5 HOH A 5 505 419 HOH HOH . 
F 5 HOH A 6 506 318 HOH HOH . 
F 5 HOH A 7 507 543 HOH HOH . 
F 5 HOH A 8 508 461 HOH HOH . 
F 5 HOH A 9 509 429 HOH HOH . 
F 5 HOH A 10 510 566 HOH HOH . 
F 5 HOH A 11 511 514 HOH HOH . 
F 5 HOH A 12 512 316 HOH HOH . 
F 5 HOH A 13 513 358 HOH HOH . 
F 5 HOH A 14 514 471 HOH HOH . 
F 5 HOH A 15 515 524 HOH HOH . 
F 5 HOH A 16 516 483 HOH HOH . 
F 5 HOH A 17 517 545 HOH HOH . 
F 5 HOH A 18 518 502 HOH HOH . 
F 5 HOH A 19 519 531 HOH HOH . 
F 5 HOH A 20 520 501 HOH HOH . 
F 5 HOH A 21 521 532 HOH HOH . 
F 5 HOH A 22 522 449 HOH HOH . 
F 5 HOH A 23 523 369 HOH HOH . 
F 5 HOH A 24 524 491 HOH HOH . 
F 5 HOH A 25 525 469 HOH HOH . 
F 5 HOH A 26 526 398 HOH HOH . 
F 5 HOH A 27 527 328 HOH HOH . 
F 5 HOH A 28 528 406 HOH HOH . 
F 5 HOH A 29 529 370 HOH HOH . 
F 5 HOH A 30 530 517 HOH HOH . 
F 5 HOH A 31 531 423 HOH HOH . 
F 5 HOH A 32 532 347 HOH HOH . 
F 5 HOH A 33 533 488 HOH HOH . 
F 5 HOH A 34 534 499 HOH HOH . 
F 5 HOH A 35 535 536 HOH HOH . 
F 5 HOH A 36 536 372 HOH HOH . 
F 5 HOH A 37 537 402 HOH HOH . 
F 5 HOH A 38 538 473 HOH HOH . 
F 5 HOH A 39 539 530 HOH HOH . 
F 5 HOH A 40 540 311 HOH HOH . 
F 5 HOH A 41 541 400 HOH HOH . 
F 5 HOH A 42 542 327 HOH HOH . 
F 5 HOH A 43 543 425 HOH HOH . 
F 5 HOH A 44 544 390 HOH HOH . 
F 5 HOH A 45 545 310 HOH HOH . 
F 5 HOH A 46 546 304 HOH HOH . 
F 5 HOH A 47 547 424 HOH HOH . 
F 5 HOH A 48 548 539 HOH HOH . 
F 5 HOH A 49 549 541 HOH HOH . 
F 5 HOH A 50 550 396 HOH HOH . 
F 5 HOH A 51 551 380 HOH HOH . 
F 5 HOH A 52 552 303 HOH HOH . 
F 5 HOH A 53 553 504 HOH HOH . 
F 5 HOH A 54 554 403 HOH HOH . 
F 5 HOH A 55 555 357 HOH HOH . 
F 5 HOH A 56 556 334 HOH HOH . 
F 5 HOH A 57 557 378 HOH HOH . 
F 5 HOH A 58 558 480 HOH HOH . 
F 5 HOH A 59 559 568 HOH HOH . 
F 5 HOH A 60 560 320 HOH HOH . 
F 5 HOH A 61 561 440 HOH HOH . 
F 5 HOH A 62 562 533 HOH HOH . 
F 5 HOH A 63 563 384 HOH HOH . 
F 5 HOH A 64 564 391 HOH HOH . 
F 5 HOH A 65 565 476 HOH HOH . 
F 5 HOH A 66 566 359 HOH HOH . 
F 5 HOH A 67 567 326 HOH HOH . 
F 5 HOH A 68 568 435 HOH HOH . 
F 5 HOH A 69 569 538 HOH HOH . 
F 5 HOH A 70 570 335 HOH HOH . 
F 5 HOH A 71 571 344 HOH HOH . 
F 5 HOH A 72 572 309 HOH HOH . 
F 5 HOH A 73 573 382 HOH HOH . 
F 5 HOH A 74 574 368 HOH HOH . 
F 5 HOH A 75 575 567 HOH HOH . 
F 5 HOH A 76 576 346 HOH HOH . 
F 5 HOH A 77 577 333 HOH HOH . 
F 5 HOH A 78 578 537 HOH HOH . 
F 5 HOH A 79 579 375 HOH HOH . 
F 5 HOH A 80 580 360 HOH HOH . 
F 5 HOH A 81 581 414 HOH HOH . 
F 5 HOH A 82 582 330 HOH HOH . 
F 5 HOH A 83 583 352 HOH HOH . 
F 5 HOH A 84 584 363 HOH HOH . 
F 5 HOH A 85 585 417 HOH HOH . 
F 5 HOH A 86 586 350 HOH HOH . 
F 5 HOH A 87 587 323 HOH HOH . 
F 5 HOH A 88 588 362 HOH HOH . 
F 5 HOH A 89 589 523 HOH HOH . 
F 5 HOH A 90 590 306 HOH HOH . 
F 5 HOH A 91 591 337 HOH HOH . 
F 5 HOH A 92 592 371 HOH HOH . 
F 5 HOH A 93 593 562 HOH HOH . 
F 5 HOH A 94 594 459 HOH HOH . 
F 5 HOH A 95 595 407 HOH HOH . 
F 5 HOH A 96 596 387 HOH HOH . 
F 5 HOH A 97 597 408 HOH HOH . 
F 5 HOH A 98 598 433 HOH HOH . 
F 5 HOH A 99 599 354 HOH HOH . 
F 5 HOH A 100 600 302 HOH HOH . 
F 5 HOH A 101 601 340 HOH HOH . 
F 5 HOH A 102 602 308 HOH HOH . 
F 5 HOH A 103 603 559 HOH HOH . 
F 5 HOH A 104 604 563 HOH HOH . 
F 5 HOH A 105 605 468 HOH HOH . 
F 5 HOH A 106 606 405 HOH HOH . 
F 5 HOH A 107 607 561 HOH HOH . 
F 5 HOH A 108 608 548 HOH HOH . 
F 5 HOH A 109 609 301 HOH HOH . 
F 5 HOH A 110 610 379 HOH HOH . 
F 5 HOH A 111 611 305 HOH HOH . 
F 5 HOH A 112 612 460 HOH HOH . 
F 5 HOH A 113 613 322 HOH HOH . 
F 5 HOH A 114 614 343 HOH HOH . 
F 5 HOH A 115 615 315 HOH HOH . 
F 5 HOH A 116 616 454 HOH HOH . 
F 5 HOH A 117 617 430 HOH HOH . 
F 5 HOH A 118 618 377 HOH HOH . 
F 5 HOH A 119 619 381 HOH HOH . 
F 5 HOH A 120 620 416 HOH HOH . 
F 5 HOH A 121 621 493 HOH HOH . 
F 5 HOH A 122 622 482 HOH HOH . 
F 5 HOH A 123 623 314 HOH HOH . 
F 5 HOH A 124 624 401 HOH HOH . 
F 5 HOH A 125 625 492 HOH HOH . 
F 5 HOH A 126 626 388 HOH HOH . 
F 5 HOH A 127 627 555 HOH HOH . 
F 5 HOH A 128 628 366 HOH HOH . 
F 5 HOH A 129 629 383 HOH HOH . 
F 5 HOH A 130 630 348 HOH HOH . 
F 5 HOH A 131 631 386 HOH HOH . 
F 5 HOH A 132 632 522 HOH HOH . 
F 5 HOH A 133 633 542 HOH HOH . 
F 5 HOH A 134 634 313 HOH HOH . 
F 5 HOH A 135 635 389 HOH HOH . 
F 5 HOH A 136 636 450 HOH HOH . 
F 5 HOH A 137 637 436 HOH HOH . 
F 5 HOH A 138 638 367 HOH HOH . 
F 5 HOH A 139 639 553 HOH HOH . 
F 5 HOH A 140 640 507 HOH HOH . 
F 5 HOH A 141 641 560 HOH HOH . 
F 5 HOH A 142 642 395 HOH HOH . 
F 5 HOH A 143 643 317 HOH HOH . 
F 5 HOH A 144 644 525 HOH HOH . 
F 5 HOH A 145 645 413 HOH HOH . 
F 5 HOH A 146 646 444 HOH HOH . 
F 5 HOH A 147 647 481 HOH HOH . 
F 5 HOH A 148 648 307 HOH HOH . 
F 5 HOH A 149 649 441 HOH HOH . 
F 5 HOH A 150 650 540 HOH HOH . 
F 5 HOH A 151 651 420 HOH HOH . 
F 5 HOH A 152 652 336 HOH HOH . 
F 5 HOH A 153 653 325 HOH HOH . 
F 5 HOH A 154 654 437 HOH HOH . 
F 5 HOH A 155 655 365 HOH HOH . 
F 5 HOH A 156 656 497 HOH HOH . 
F 5 HOH A 157 657 341 HOH HOH . 
F 5 HOH A 158 658 513 HOH HOH . 
F 5 HOH A 159 659 321 HOH HOH . 
F 5 HOH A 160 660 409 HOH HOH . 
F 5 HOH A 161 661 556 HOH HOH . 
F 5 HOH A 162 662 373 HOH HOH . 
F 5 HOH A 163 663 329 HOH HOH . 
F 5 HOH A 164 664 339 HOH HOH . 
F 5 HOH A 165 665 410 HOH HOH . 
F 5 HOH A 166 666 544 HOH HOH . 
F 5 HOH A 167 667 404 HOH HOH . 
F 5 HOH A 168 668 508 HOH HOH . 
F 5 HOH A 169 669 451 HOH HOH . 
F 5 HOH A 170 670 498 HOH HOH . 
F 5 HOH A 171 671 500 HOH HOH . 
F 5 HOH A 172 672 385 HOH HOH . 
F 5 HOH A 173 673 564 HOH HOH . 
F 5 HOH A 174 674 356 HOH HOH . 
F 5 HOH A 175 675 319 HOH HOH . 
F 5 HOH A 176 676 472 HOH HOH . 
F 5 HOH A 177 677 448 HOH HOH . 
F 5 HOH A 178 678 324 HOH HOH . 
F 5 HOH A 179 679 554 HOH HOH . 
F 5 HOH A 180 680 475 HOH HOH . 
F 5 HOH A 181 681 535 HOH HOH . 
F 5 HOH A 182 682 519 HOH HOH . 
F 5 HOH A 183 683 458 HOH HOH . 
F 5 HOH A 184 684 434 HOH HOH . 
F 5 HOH A 185 685 565 HOH HOH . 
F 5 HOH A 186 686 456 HOH HOH . 
F 5 HOH A 187 687 465 HOH HOH . 
F 5 HOH A 188 688 443 HOH HOH . 
F 5 HOH A 189 689 547 HOH HOH . 
F 5 HOH A 190 690 355 HOH HOH . 
F 5 HOH A 191 691 558 HOH HOH . 
F 5 HOH A 192 692 427 HOH HOH . 
F 5 HOH A 193 693 374 HOH HOH . 
F 5 HOH A 194 694 426 HOH HOH . 
F 5 HOH A 195 695 438 HOH HOH . 
F 5 HOH A 196 696 431 HOH HOH . 
F 5 HOH A 197 697 364 HOH HOH . 
F 5 HOH A 198 698 466 HOH HOH . 
F 5 HOH A 199 699 487 HOH HOH . 
F 5 HOH A 200 700 557 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 3 102.995 100.31 -8.24 1 75.7 ? C1 GOL 402 A 1 
HETATM 2 O O1 GOL . . . D 3 102.037 100.993 -9.049 1 56.61 ? O1 GOL 402 A 1 
HETATM 3 C C2 GOL . . . D 3 104.161 99.811 -9.07 1 70.79 ? C2 GOL 402 A 1 
HETATM 4 O O2 GOL . . . D 3 103.997 98.407 -9.281 1 97.62 ? O2 GOL 402 A 1 
HETATM 5 C C3 GOL . . . D 3 105.539 100.115 -8.501 1 87.57 ? C3 GOL 402 A 1 
HETATM 6 O O3 GOL . . . D 3 106.518 100.336 -9.523 1 84 ? O3 GOL 402 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           316 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           6 
#