data_5YIB
#
_model_server_result.job_id            3uyz-UF3vXDgDTD1dSLUkw 
_model_server_result.datetime_utc      '2024-11-08 13:45:40' 
_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          5yib 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":406}' 
#
_entry.id    5YIB 
#
_exptl.entry_id    5YIB 
_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    5 
_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            5YIB 
_cell.length_a            106.25 
_cell.length_b            106.25 
_cell.length_c            70.85 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YIB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        79 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 4' 
#
_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,G,H,I,J,K 
_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 
? 3 E N N 
? 3 F N N 
? 3 G 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 46 A CYS 49 1_555 A SG CYS 51 A CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
disulf ? disulf2 A SG CYS 248 A CYS 251 1_555 A SG CYS 284 A CYS 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
#
_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 
#
_atom_sites.entry_id                     5YIB 
_atom_sites.fract_transf_matrix[1][1]    0.009412 
_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]    0.009412 
_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]    0.014114 
_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 8VC A 1 401 2 8VC 743 . 
C 3 GOL A 1 402 1 GOL GOL . 
D 3 GOL A 1 403 3 GOL GOL . 
E 3 GOL A 1 404 4 GOL GOL . 
F 3 GOL A 1 405 6 GOL GOL . 
G 3 GOL A 1 406 7 GOL GOL . 
H 4 EDO A 1 407 1 EDO EDO . 
I 4 EDO A 1 408 2 EDO EDO . 
J 5 CPS A 1 409 1 CPS CPS . 
K 6 HOH A 1 501 101 HOH HOH . 
K 6 HOH A 2 502 31 HOH HOH . 
K 6 HOH A 3 503 45 HOH HOH . 
K 6 HOH A 4 504 55 HOH HOH . 
K 6 HOH A 5 505 100 HOH HOH . 
K 6 HOH A 6 506 98 HOH HOH . 
K 6 HOH A 7 507 120 HOH HOH . 
K 6 HOH A 8 508 103 HOH HOH . 
K 6 HOH A 9 509 8 HOH HOH . 
K 6 HOH A 10 510 20 HOH HOH . 
K 6 HOH A 11 511 67 HOH HOH . 
K 6 HOH A 12 512 51 HOH HOH . 
K 6 HOH A 13 513 113 HOH HOH . 
K 6 HOH A 14 514 35 HOH HOH . 
K 6 HOH A 15 515 48 HOH HOH . 
K 6 HOH A 16 516 6 HOH HOH . 
K 6 HOH A 17 517 34 HOH HOH . 
K 6 HOH A 18 518 66 HOH HOH . 
K 6 HOH A 19 519 96 HOH HOH . 
K 6 HOH A 20 520 26 HOH HOH . 
K 6 HOH A 21 521 30 HOH HOH . 
K 6 HOH A 22 522 15 HOH HOH . 
K 6 HOH A 23 523 33 HOH HOH . 
K 6 HOH A 24 524 52 HOH HOH . 
K 6 HOH A 25 525 11 HOH HOH . 
K 6 HOH A 26 526 105 HOH HOH . 
K 6 HOH A 27 527 12 HOH HOH . 
K 6 HOH A 28 528 54 HOH HOH . 
K 6 HOH A 29 529 97 HOH HOH . 
K 6 HOH A 30 530 102 HOH HOH . 
K 6 HOH A 31 531 64 HOH HOH . 
K 6 HOH A 32 532 17 HOH HOH . 
K 6 HOH A 33 533 43 HOH HOH . 
K 6 HOH A 34 534 42 HOH HOH . 
K 6 HOH A 35 535 108 HOH HOH . 
K 6 HOH A 36 536 19 HOH HOH . 
K 6 HOH A 37 537 7 HOH HOH . 
K 6 HOH A 38 538 111 HOH HOH . 
K 6 HOH A 39 539 13 HOH HOH . 
K 6 HOH A 40 540 122 HOH HOH . 
K 6 HOH A 41 541 53 HOH HOH . 
K 6 HOH A 42 542 121 HOH HOH . 
K 6 HOH A 43 543 41 HOH HOH . 
K 6 HOH A 44 544 4 HOH HOH . 
K 6 HOH A 45 545 65 HOH HOH . 
K 6 HOH A 46 546 78 HOH HOH . 
K 6 HOH A 47 547 5 HOH HOH . 
K 6 HOH A 48 548 24 HOH HOH . 
K 6 HOH A 49 549 18 HOH HOH . 
K 6 HOH A 50 550 29 HOH HOH . 
K 6 HOH A 51 551 73 HOH HOH . 
K 6 HOH A 52 552 124 HOH HOH . 
K 6 HOH A 53 553 36 HOH HOH . 
K 6 HOH A 54 554 10 HOH HOH . 
K 6 HOH A 55 555 2 HOH HOH . 
K 6 HOH A 56 556 14 HOH HOH . 
K 6 HOH A 57 557 123 HOH HOH . 
K 6 HOH A 58 558 115 HOH HOH . 
K 6 HOH A 59 559 86 HOH HOH . 
K 6 HOH A 60 560 38 HOH HOH . 
K 6 HOH A 61 561 25 HOH HOH . 
K 6 HOH A 62 562 79 HOH HOH . 
K 6 HOH A 63 563 77 HOH HOH . 
K 6 HOH A 64 564 47 HOH HOH . 
K 6 HOH A 65 565 40 HOH HOH . 
K 6 HOH A 66 566 21 HOH HOH . 
K 6 HOH A 67 567 99 HOH HOH . 
K 6 HOH A 68 568 9 HOH HOH . 
K 6 HOH A 69 569 137 HOH HOH . 
K 6 HOH A 70 570 60 HOH HOH . 
K 6 HOH A 71 571 95 HOH HOH . 
K 6 HOH A 72 572 39 HOH HOH . 
K 6 HOH A 73 573 82 HOH HOH . 
K 6 HOH A 74 574 76 HOH HOH . 
K 6 HOH A 75 575 118 HOH HOH . 
K 6 HOH A 76 576 125 HOH HOH . 
K 6 HOH A 77 577 112 HOH HOH . 
K 6 HOH A 78 578 16 HOH HOH . 
K 6 HOH A 79 579 50 HOH HOH . 
K 6 HOH A 80 580 136 HOH HOH . 
K 6 HOH A 81 581 68 HOH HOH . 
K 6 HOH A 82 582 28 HOH HOH . 
K 6 HOH A 83 583 27 HOH HOH . 
K 6 HOH A 84 584 72 HOH HOH . 
K 6 HOH A 85 585 22 HOH HOH . 
K 6 HOH A 86 586 32 HOH HOH . 
K 6 HOH A 87 587 109 HOH HOH . 
K 6 HOH A 88 588 135 HOH HOH . 
K 6 HOH A 89 589 114 HOH HOH . 
K 6 HOH A 90 590 37 HOH HOH . 
K 6 HOH A 91 591 107 HOH HOH . 
K 6 HOH A 92 592 88 HOH HOH . 
K 6 HOH A 93 593 69 HOH HOH . 
K 6 HOH A 94 594 44 HOH HOH . 
K 6 HOH A 95 595 133 HOH HOH . 
K 6 HOH A 96 596 58 HOH HOH . 
K 6 HOH A 97 597 62 HOH HOH . 
K 6 HOH A 98 598 74 HOH HOH . 
K 6 HOH A 99 599 23 HOH HOH . 
K 6 HOH A 100 600 132 HOH HOH . 
K 6 HOH A 101 601 1 HOH HOH . 
K 6 HOH A 102 602 93 HOH HOH . 
K 6 HOH A 103 603 89 HOH HOH . 
K 6 HOH A 104 604 3 HOH HOH . 
K 6 HOH A 105 605 110 HOH HOH . 
K 6 HOH A 106 606 63 HOH HOH . 
K 6 HOH A 107 607 57 HOH HOH . 
K 6 HOH A 108 608 134 HOH HOH . 
K 6 HOH A 109 609 116 HOH HOH . 
K 6 HOH A 110 610 71 HOH HOH . 
K 6 HOH A 111 611 131 HOH HOH . 
K 6 HOH A 112 612 119 HOH HOH . 
K 6 HOH A 113 613 80 HOH HOH . 
K 6 HOH A 114 614 128 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 . . . G 3 2.708 -31.365 -41.533 1 81.14 ? C1 GOL 406 A 1 
HETATM 2 O O1 GOL . . . G 3 1.726 -30.34 -41.731 1 80.28 ? O1 GOL 406 A 1 
HETATM 3 C C2 GOL . . . G 3 3.05 -32.01 -42.874 1 82.09 ? C2 GOL 406 A 1 
HETATM 4 O O2 GOL . . . G 3 3.991 -31.176 -43.557 1 81.92 ? O2 GOL 406 A 1 
HETATM 5 C C3 GOL . . . G 3 3.677 -33.396 -42.702 1 83.39 ? C3 GOL 406 A 1 
HETATM 6 O O3 GOL . . . G 3 2.746 -34.373 -42.223 1 83.07 ? O3 GOL 406 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           307 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           6 
#