data_5YHV
#
_model_server_result.job_id            oJJEjY20gUWHiiIlEcfQhg 
_model_server_result.datetime_utc      '2025-03-12 04:28:28' 
_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          5yhv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":402}' 
#
_entry.id    5YHV 
#
_exptl.entry_id    5YHV 
_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    3 
_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            5YHV 
_cell.length_a            93.277 
_cell.length_b            98.224 
_cell.length_c            198.774 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YHV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,P,Q,R 
_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 F N N 
? 3 I N N 
? 3 K 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 NZ LYS 240 A LYS 234 1_555 G C4A PLP . A PLP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.563 ? 
covale ? covale2 B NZ LYS 240 B LYS 234 1_555 H C4A PLP . B PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.574 ? 
covale ? covale3 C NZ LYS 240 C LYS 234 1_555 M C4A PLP . C PLP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.6 ? 
covale ? covale4 D NZ LYS 240 D LYS 234 1_555 N C4A PLP . D PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.571 ? 
#
_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 144 n n 
C1 C2 GOL sing 145 n n 
C1 H11 GOL sing 146 n n 
C1 H12 GOL sing 147 n n 
O1 HO1 GOL sing 148 n n 
C2 O2 GOL sing 149 n n 
C2 C3 GOL sing 150 n n 
C2 H2 GOL sing 151 n n 
O2 HO2 GOL sing 152 n n 
C3 O3 GOL sing 153 n n 
C3 H31 GOL sing 154 n n 
C3 H32 GOL sing 155 n n 
O3 HO3 GOL sing 156 n n 
#
_atom_sites.entry_id                     5YHV 
_atom_sites.fract_transf_matrix[1][1]    0.010721 
_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]    0.010181 
_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]    0.005031 
_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 2 GLU A 1 401 389 GLU GLU . 
F 3 GOL A 1 402 390 GOL GOL . 
G 4 PLP A 1 403 391 PLP PLP . 
H 4 PLP B 1 401 389 PLP PLP . 
I 3 GOL B 1 402 390 GOL GOL . 
J 5 AKG B 1 403 391 AKG AKG . 
K 3 GOL C 1 401 389 GOL GOL . 
L 5 AKG C 1 402 390 AKG AKG . 
M 4 PLP C 1 403 391 PLP PLP . 
N 4 PLP D 1 401 380 PLP PLP . 
O 6 HOH A 1 501 400 HOH HOH . 
O 6 HOH A 2 502 394 HOH HOH . 
O 6 HOH A 3 503 423 HOH HOH . 
O 6 HOH A 4 504 392 HOH HOH . 
O 6 HOH A 5 505 417 HOH HOH . 
O 6 HOH A 6 506 429 HOH HOH . 
O 6 HOH A 7 507 454 HOH HOH . 
O 6 HOH A 8 508 434 HOH HOH . 
O 6 HOH A 9 509 422 HOH HOH . 
O 6 HOH A 10 510 425 HOH HOH . 
O 6 HOH A 11 511 468 HOH HOH . 
O 6 HOH A 12 512 402 HOH HOH . 
O 6 HOH A 13 513 450 HOH HOH . 
O 6 HOH A 14 514 395 HOH HOH . 
O 6 HOH A 15 515 411 HOH HOH . 
O 6 HOH A 16 516 397 HOH HOH . 
O 6 HOH A 17 517 444 HOH HOH . 
O 6 HOH A 18 518 458 HOH HOH . 
O 6 HOH A 19 519 451 HOH HOH . 
O 6 HOH A 20 520 403 HOH HOH . 
O 6 HOH A 21 521 442 HOH HOH . 
O 6 HOH A 22 522 396 HOH HOH . 
O 6 HOH A 23 523 437 HOH HOH . 
O 6 HOH A 24 524 431 HOH HOH . 
O 6 HOH A 25 525 464 HOH HOH . 
O 6 HOH A 26 526 415 HOH HOH . 
O 6 HOH A 27 527 416 HOH HOH . 
O 6 HOH A 28 528 441 HOH HOH . 
O 6 HOH A 29 529 419 HOH HOH . 
O 6 HOH A 30 530 460 HOH HOH . 
O 6 HOH A 31 531 401 HOH HOH . 
O 6 HOH A 32 532 404 HOH HOH . 
O 6 HOH A 33 533 448 HOH HOH . 
O 6 HOH A 34 534 412 HOH HOH . 
O 6 HOH A 35 535 432 HOH HOH . 
O 6 HOH A 36 536 393 HOH HOH . 
O 6 HOH A 37 537 418 HOH HOH . 
O 6 HOH A 38 538 408 HOH HOH . 
O 6 HOH A 39 539 455 HOH HOH . 
O 6 HOH A 40 540 452 HOH HOH . 
O 6 HOH A 41 541 406 HOH HOH . 
O 6 HOH A 42 542 405 HOH HOH . 
O 6 HOH A 43 543 453 HOH HOH . 
O 6 HOH A 44 544 414 HOH HOH . 
O 6 HOH A 45 545 446 HOH HOH . 
O 6 HOH A 46 546 439 HOH HOH . 
O 6 HOH A 47 547 398 HOH HOH . 
O 6 HOH A 48 548 445 HOH HOH . 
O 6 HOH A 49 549 443 HOH HOH . 
O 6 HOH A 50 550 435 HOH HOH . 
O 6 HOH A 51 551 409 HOH HOH . 
O 6 HOH A 52 552 433 HOH HOH . 
O 6 HOH A 53 553 399 HOH HOH . 
O 6 HOH A 54 554 438 HOH HOH . 
O 6 HOH A 55 555 449 HOH HOH . 
O 6 HOH A 56 556 426 HOH HOH . 
O 6 HOH A 57 557 447 HOH HOH . 
O 6 HOH A 58 558 428 HOH HOH . 
O 6 HOH A 59 559 410 HOH HOH . 
O 6 HOH A 60 560 456 HOH HOH . 
O 6 HOH A 61 561 467 HOH HOH . 
O 6 HOH A 62 562 459 HOH HOH . 
O 6 HOH A 63 563 466 HOH HOH . 
O 6 HOH A 64 564 465 HOH HOH . 
O 6 HOH A 65 565 461 HOH HOH . 
O 6 HOH A 66 566 413 HOH HOH . 
O 6 HOH A 67 567 469 HOH HOH . 
O 6 HOH A 68 568 462 HOH HOH . 
O 6 HOH A 69 569 420 HOH HOH . 
O 6 HOH A 70 570 427 HOH HOH . 
O 6 HOH A 71 571 436 HOH HOH . 
O 6 HOH A 72 572 421 HOH HOH . 
O 6 HOH A 73 573 440 HOH HOH . 
O 6 HOH A 74 574 396 HOH HOH . 
O 6 HOH A 75 575 463 HOH HOH . 
O 6 HOH A 76 576 435 HOH HOH . 
O 6 HOH A 77 577 424 HOH HOH . 
O 6 HOH A 78 578 407 HOH HOH . 
O 6 HOH A 79 579 430 HOH HOH . 
P 6 HOH B 1 501 446 HOH HOH . 
P 6 HOH B 2 502 455 HOH HOH . 
P 6 HOH B 3 503 452 HOH HOH . 
P 6 HOH B 4 504 395 HOH HOH . 
P 6 HOH B 5 505 393 HOH HOH . 
P 6 HOH B 6 506 450 HOH HOH . 
P 6 HOH B 7 507 417 HOH HOH . 
P 6 HOH B 8 508 414 HOH HOH . 
P 6 HOH B 9 509 437 HOH HOH . 
P 6 HOH B 10 510 416 HOH HOH . 
P 6 HOH B 11 511 444 HOH HOH . 
P 6 HOH B 12 512 415 HOH HOH . 
P 6 HOH B 13 513 412 HOH HOH . 
P 6 HOH B 14 514 402 HOH HOH . 
P 6 HOH B 15 515 410 HOH HOH . 
P 6 HOH B 16 516 433 HOH HOH . 
P 6 HOH B 17 517 401 HOH HOH . 
P 6 HOH B 18 518 430 HOH HOH . 
P 6 HOH B 19 519 427 HOH HOH . 
P 6 HOH B 20 520 408 HOH HOH . 
P 6 HOH B 21 521 438 HOH HOH . 
P 6 HOH B 22 522 396 HOH HOH . 
P 6 HOH B 23 523 394 HOH HOH . 
P 6 HOH B 24 524 442 HOH HOH . 
P 6 HOH B 25 525 453 HOH HOH . 
P 6 HOH B 26 526 392 HOH HOH . 
P 6 HOH B 27 527 407 HOH HOH . 
P 6 HOH B 28 528 432 HOH HOH . 
P 6 HOH B 29 529 411 HOH HOH . 
P 6 HOH B 30 530 440 HOH HOH . 
P 6 HOH B 31 531 419 HOH HOH . 
P 6 HOH B 32 532 456 HOH HOH . 
P 6 HOH B 33 533 400 HOH HOH . 
P 6 HOH B 34 534 404 HOH HOH . 
P 6 HOH B 35 535 462 HOH HOH . 
P 6 HOH B 36 536 398 HOH HOH . 
P 6 HOH B 37 537 428 HOH HOH . 
P 6 HOH B 38 538 406 HOH HOH . 
P 6 HOH B 39 539 448 HOH HOH . 
P 6 HOH B 40 540 461 HOH HOH . 
P 6 HOH B 41 541 397 HOH HOH . 
P 6 HOH B 42 542 403 HOH HOH . 
P 6 HOH B 43 543 431 HOH HOH . 
P 6 HOH B 44 544 464 HOH HOH . 
P 6 HOH B 45 545 459 HOH HOH . 
P 6 HOH B 46 546 436 HOH HOH . 
P 6 HOH B 47 547 409 HOH HOH . 
P 6 HOH B 48 548 421 HOH HOH . 
P 6 HOH B 49 549 425 HOH HOH . 
P 6 HOH B 50 550 451 HOH HOH . 
P 6 HOH B 51 551 439 HOH HOH . 
P 6 HOH B 52 552 447 HOH HOH . 
P 6 HOH B 53 553 465 HOH HOH . 
P 6 HOH B 54 554 434 HOH HOH . 
P 6 HOH B 55 555 429 HOH HOH . 
P 6 HOH B 56 556 399 HOH HOH . 
P 6 HOH B 57 557 418 HOH HOH . 
P 6 HOH B 58 558 454 HOH HOH . 
P 6 HOH B 59 559 458 HOH HOH . 
P 6 HOH B 60 560 449 HOH HOH . 
P 6 HOH B 61 561 426 HOH HOH . 
P 6 HOH B 62 562 420 HOH HOH . 
P 6 HOH B 63 563 460 HOH HOH . 
P 6 HOH B 64 564 463 HOH HOH . 
P 6 HOH B 65 565 413 HOH HOH . 
P 6 HOH B 66 566 405 HOH HOH . 
P 6 HOH B 67 567 441 HOH HOH . 
P 6 HOH B 68 568 457 HOH HOH . 
P 6 HOH B 69 569 424 HOH HOH . 
P 6 HOH B 70 570 443 HOH HOH . 
P 6 HOH B 71 571 423 HOH HOH . 
P 6 HOH B 72 572 422 HOH HOH . 
P 6 HOH B 73 573 445 HOH HOH . 
Q 6 HOH C 1 501 412 HOH HOH . 
Q 6 HOH C 2 502 393 HOH HOH . 
Q 6 HOH C 3 503 421 HOH HOH . 
Q 6 HOH C 4 504 403 HOH HOH . 
Q 6 HOH C 5 505 395 HOH HOH . 
Q 6 HOH C 6 506 420 HOH HOH . 
Q 6 HOH C 7 507 407 HOH HOH . 
Q 6 HOH C 8 508 406 HOH HOH . 
Q 6 HOH C 9 509 416 HOH HOH . 
Q 6 HOH C 10 510 419 HOH HOH . 
Q 6 HOH C 11 511 400 HOH HOH . 
Q 6 HOH C 12 512 424 HOH HOH . 
Q 6 HOH C 13 513 409 HOH HOH . 
Q 6 HOH C 14 514 402 HOH HOH . 
Q 6 HOH C 15 515 398 HOH HOH . 
Q 6 HOH C 16 516 408 HOH HOH . 
Q 6 HOH C 17 517 411 HOH HOH . 
Q 6 HOH C 18 518 417 HOH HOH . 
Q 6 HOH C 19 519 399 HOH HOH . 
Q 6 HOH C 20 520 392 HOH HOH . 
Q 6 HOH C 21 521 401 HOH HOH . 
Q 6 HOH C 22 522 405 HOH HOH . 
Q 6 HOH C 23 523 413 HOH HOH . 
Q 6 HOH C 24 524 410 HOH HOH . 
Q 6 HOH C 25 525 418 HOH HOH . 
Q 6 HOH C 26 526 425 HOH HOH . 
Q 6 HOH C 27 527 422 HOH HOH . 
Q 6 HOH C 28 528 404 HOH HOH . 
Q 6 HOH C 29 529 397 HOH HOH . 
Q 6 HOH C 30 530 414 HOH HOH . 
Q 6 HOH C 31 531 457 HOH HOH . 
Q 6 HOH C 32 532 415 HOH HOH . 
Q 6 HOH C 33 533 394 HOH HOH . 
Q 6 HOH C 34 534 426 HOH HOH . 
R 6 HOH D 1 501 393 HOH HOH . 
R 6 HOH D 2 502 392 HOH HOH . 
R 6 HOH D 3 503 385 HOH HOH . 
R 6 HOH D 4 504 390 HOH HOH . 
R 6 HOH D 5 505 382 HOH HOH . 
R 6 HOH D 6 506 384 HOH HOH . 
R 6 HOH D 7 507 388 HOH HOH . 
R 6 HOH D 8 508 386 HOH HOH . 
R 6 HOH D 9 509 389 HOH HOH . 
R 6 HOH D 10 510 394 HOH HOH . 
R 6 HOH D 11 511 387 HOH HOH . 
R 6 HOH D 12 512 391 HOH HOH . 
R 6 HOH D 13 513 383 HOH HOH . 
R 6 HOH D 14 514 381 HOH HOH . 
R 6 HOH D 15 515 423 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 . . . I 3 -54.645 -46.288 13.39 1 66.23 ? C1 GOL 402 B 1 
HETATM 2 O O1 GOL . . . I 3 -53.263 -45.904 13.477 1 64.26 ? O1 GOL 402 B 1 
HETATM 3 C C2 GOL . . . I 3 -54.981 -46.83 12.001 1 65.37 ? C2 GOL 402 B 1 
HETATM 4 O O2 GOL . . . I 3 -55.178 -48.249 12.08 1 65.85 ? O2 GOL 402 B 1 
HETATM 5 C C3 GOL . . . I 3 -56.243 -46.154 11.466 1 65.71 ? C3 GOL 402 B 1 
HETATM 6 O O3 GOL . . . I 3 -56.597 -46.704 10.19 1 63.72 ? O3 GOL 402 B 1 
#
_model_server_stats.io_time_ms              24 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    39 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           6 
#