data_5Y2F
#
_model_server_result.job_id            Ya6CX9gck-VS7n6zSuM_aw 
_model_server_result.datetime_utc      '2024-11-18 21:34:26' 
_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          5y2f 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":406}' 
#
_entry.id    5Y2F 
#
_exptl.entry_id    5Y2F 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          6 
_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            5Y2F 
_cell.length_a            162.422 
_cell.length_b            162.422 
_cell.length_c            162.422 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5Y2F 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        213 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 3 2' 
#
_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 
#
_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,S,T,U 
_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 F N N 
? 6 G N N 
? 6 H N N 
? 6 I 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
metalc ? metalc1 A SG CYS 139 A CYS 139 1_555 E ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? 
metalc ? metalc2 A SG CYS 142 A CYS 142 1_555 E ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? 
metalc ? metalc3 A SG CYS 164 A CYS 164 1_555 E ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
metalc ? metalc4 A SG CYS 175 A CYS 175 1_555 E ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? 
covale ? covale1 B NZ LYS 5 C LYS 5 1_555 R C1 HDR . C HDR 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? 
#
_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                     5Y2F 
_atom_sites.fract_transf_matrix[1][1]    0.006157 
_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]    0.006157 
_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]    0.006157 
_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 AR6 A 1 401 1 AR6 AR6 . 
D 4 8L9 A 1 402 1 8L9 318 . 
E 5 ZN A 1 403 1 ZN ZN . 
F 6 GOL A 1 404 1 GOL GOL . 
G 6 GOL A 1 405 2 GOL GOL . 
H 6 GOL A 1 406 3 GOL GOL . 
I 6 GOL A 1 407 4 GOL GOL . 
J 6 GOL A 1 408 5 GOL GOL . 
K 7 SO4 A 1 409 6 SO4 SO4 . 
L 7 SO4 A 1 410 7 SO4 SO4 . 
M 7 SO4 A 1 411 8 SO4 SO4 . 
N 7 SO4 A 1 412 10 SO4 SO4 . 
O 7 SO4 A 1 413 11 SO4 SO4 . 
P 7 SO4 A 1 414 12 SO4 SO4 . 
Q 8 PEG A 1 415 13 PEG PEG . 
R 9 HDR C 1 101 1 HDR MYR . 
S 7 SO4 C 1 102 9 SO4 SO4 . 
T 10 HOH A 1 501 1 HOH HOH . 
T 10 HOH A 2 502 87 HOH HOH . 
T 10 HOH A 3 503 108 HOH HOH . 
T 10 HOH A 4 504 4 HOH HOH . 
T 10 HOH A 5 505 25 HOH HOH . 
T 10 HOH A 6 506 98 HOH HOH . 
T 10 HOH A 7 507 9 HOH HOH . 
T 10 HOH A 8 508 68 HOH HOH . 
T 10 HOH A 9 509 91 HOH HOH . 
T 10 HOH A 10 510 47 HOH HOH . 
T 10 HOH A 11 511 28 HOH HOH . 
T 10 HOH A 12 512 3 HOH HOH . 
T 10 HOH A 13 513 73 HOH HOH . 
T 10 HOH A 14 514 115 HOH HOH . 
T 10 HOH A 15 515 8 HOH HOH . 
T 10 HOH A 16 516 33 HOH HOH . 
T 10 HOH A 17 517 6 HOH HOH . 
T 10 HOH A 18 518 74 HOH HOH . 
T 10 HOH A 19 519 66 HOH HOH . 
T 10 HOH A 20 520 30 HOH HOH . 
T 10 HOH A 21 521 75 HOH HOH . 
T 10 HOH A 22 522 43 HOH HOH . 
T 10 HOH A 23 523 76 HOH HOH . 
T 10 HOH A 24 524 45 HOH HOH . 
T 10 HOH A 25 525 80 HOH HOH . 
T 10 HOH A 26 526 50 HOH HOH . 
T 10 HOH A 27 527 67 HOH HOH . 
T 10 HOH A 28 528 11 HOH HOH . 
T 10 HOH A 29 529 5 HOH HOH . 
T 10 HOH A 30 530 22 HOH HOH . 
T 10 HOH A 31 531 34 HOH HOH . 
T 10 HOH A 32 532 127 HOH HOH . 
T 10 HOH A 33 533 71 HOH HOH . 
T 10 HOH A 34 534 53 HOH HOH . 
T 10 HOH A 35 535 100 HOH HOH . 
T 10 HOH A 36 536 37 HOH HOH . 
T 10 HOH A 37 537 62 HOH HOH . 
T 10 HOH A 38 538 26 HOH HOH . 
T 10 HOH A 39 539 113 HOH HOH . 
T 10 HOH A 40 540 58 HOH HOH . 
T 10 HOH A 41 541 17 HOH HOH . 
T 10 HOH A 42 542 70 HOH HOH . 
T 10 HOH A 43 543 104 HOH HOH . 
T 10 HOH A 44 544 51 HOH HOH . 
T 10 HOH A 45 545 49 HOH HOH . 
T 10 HOH A 46 546 112 HOH HOH . 
T 10 HOH A 47 547 134 HOH HOH . 
T 10 HOH A 48 548 39 HOH HOH . 
T 10 HOH A 49 549 10 HOH HOH . 
T 10 HOH A 50 550 97 HOH HOH . 
T 10 HOH A 51 551 96 HOH HOH . 
T 10 HOH A 52 552 122 HOH HOH . 
T 10 HOH A 53 553 31 HOH HOH . 
T 10 HOH A 54 554 12 HOH HOH . 
T 10 HOH A 55 555 52 HOH HOH . 
T 10 HOH A 56 556 72 HOH HOH . 
T 10 HOH A 57 557 21 HOH HOH . 
T 10 HOH A 58 558 55 HOH HOH . 
T 10 HOH A 59 559 23 HOH HOH . 
T 10 HOH A 60 560 84 HOH HOH . 
T 10 HOH A 61 561 105 HOH HOH . 
T 10 HOH A 62 562 142 HOH HOH . 
T 10 HOH A 63 563 110 HOH HOH . 
T 10 HOH A 64 564 24 HOH HOH . 
T 10 HOH A 65 565 7 HOH HOH . 
T 10 HOH A 66 566 36 HOH HOH . 
T 10 HOH A 67 567 65 HOH HOH . 
T 10 HOH A 68 568 42 HOH HOH . 
T 10 HOH A 69 569 16 HOH HOH . 
T 10 HOH A 70 570 102 HOH HOH . 
T 10 HOH A 71 571 114 HOH HOH . 
T 10 HOH A 72 572 77 HOH HOH . 
T 10 HOH A 73 573 20 HOH HOH . 
T 10 HOH A 74 574 35 HOH HOH . 
T 10 HOH A 75 575 83 HOH HOH . 
T 10 HOH A 76 576 2 HOH HOH . 
T 10 HOH A 77 577 40 HOH HOH . 
T 10 HOH A 78 578 41 HOH HOH . 
T 10 HOH A 79 579 90 HOH HOH . 
T 10 HOH A 80 580 29 HOH HOH . 
T 10 HOH A 81 581 128 HOH HOH . 
T 10 HOH A 82 582 94 HOH HOH . 
T 10 HOH A 83 583 32 HOH HOH . 
T 10 HOH A 84 584 116 HOH HOH . 
T 10 HOH A 85 585 109 HOH HOH . 
T 10 HOH A 86 586 54 HOH HOH . 
T 10 HOH A 87 587 99 HOH HOH . 
T 10 HOH A 88 588 56 HOH HOH . 
T 10 HOH A 89 589 93 HOH HOH . 
T 10 HOH A 90 590 135 HOH HOH . 
T 10 HOH A 91 591 46 HOH HOH . 
T 10 HOH A 92 592 48 HOH HOH . 
T 10 HOH A 93 593 89 HOH HOH . 
T 10 HOH A 94 594 27 HOH HOH . 
T 10 HOH A 95 595 61 HOH HOH . 
T 10 HOH A 96 596 19 HOH HOH . 
T 10 HOH A 97 597 59 HOH HOH . 
T 10 HOH A 98 598 13 HOH HOH . 
T 10 HOH A 99 599 78 HOH HOH . 
T 10 HOH A 100 600 44 HOH HOH . 
T 10 HOH A 101 601 92 HOH HOH . 
T 10 HOH A 102 602 38 HOH HOH . 
T 10 HOH A 103 603 138 HOH HOH . 
T 10 HOH A 104 604 81 HOH HOH . 
T 10 HOH A 105 605 119 HOH HOH . 
T 10 HOH A 106 606 60 HOH HOH . 
T 10 HOH A 107 607 143 HOH HOH . 
T 10 HOH A 108 608 15 HOH HOH . 
T 10 HOH A 109 609 82 HOH HOH . 
T 10 HOH A 110 610 117 HOH HOH . 
T 10 HOH A 111 611 129 HOH HOH . 
T 10 HOH A 112 612 85 HOH HOH . 
T 10 HOH A 113 613 137 HOH HOH . 
T 10 HOH A 114 614 145 HOH HOH . 
T 10 HOH A 115 615 64 HOH HOH . 
T 10 HOH A 116 616 111 HOH HOH . 
T 10 HOH A 117 617 101 HOH HOH . 
T 10 HOH A 118 618 139 HOH HOH . 
T 10 HOH A 119 619 144 HOH HOH . 
T 10 HOH A 120 620 103 HOH HOH . 
T 10 HOH A 121 621 63 HOH HOH . 
T 10 HOH A 122 622 69 HOH HOH . 
T 10 HOH A 123 623 106 HOH HOH . 
T 10 HOH A 124 624 57 HOH HOH . 
T 10 HOH A 125 625 88 HOH HOH . 
U 10 HOH C 1 201 107 HOH HOH . 
U 10 HOH C 2 202 124 HOH HOH . 
U 10 HOH C 3 203 125 HOH HOH . 
U 10 HOH C 4 204 95 HOH HOH . 
U 10 HOH C 5 205 136 HOH HOH . 
U 10 HOH C 6 206 14 HOH HOH . 
U 10 HOH C 7 207 86 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 . . . H 6 12.279 160.712 144.092 1 137.33 ? C1 GOL 406 A 1 
HETATM 2 O O1 GOL . . . H 6 10.979 161.091 143.623 1 133.39 ? O1 GOL 406 A 1 
HETATM 3 C C2 GOL . . . H 6 12.456 159.191 143.973 1 137.46 ? C2 GOL 406 A 1 
HETATM 4 O O2 GOL . . . H 6 13.441 158.852 142.991 1 139.6 ? O2 GOL 406 A 1 
HETATM 5 C C3 GOL . . . H 6 12.876 158.577 145.309 1 132.79 ? C3 GOL 406 A 1 
HETATM 6 O O3 GOL . . . H 6 14.059 159.213 145.802 1 132.05 ? O3 GOL 406 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           251 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           6 
#