data_3VAG
#
_model_server_result.job_id            7TAKEt77g2KD81tBaTK04w 
_model_server_result.datetime_utc      '2024-12-23 09:30:33' 
_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          3vag 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":408}' 
#
_entry.id    3VAG 
#
_exptl.entry_id    3VAG 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          5 
_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          125.35 
_cell.angle_gamma         90 
_cell.entry_id            3VAG 
_cell.length_a            166.825 
_cell.length_b            37.499 
_cell.length_c            100.925 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VAG 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_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,V,W,X 
_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
? 5 L N N 
? 5 T 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 C O3' DC 2 P DC 2 1_555 C P BRU 3 P BRU 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.607 ? 
covale ? covale2 C O3' BRU 3 P BRU 3 1_555 C P DU 4 P DU 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.608 ? 
covale ? covale3 D O3' DC 2 E DC 3 1_555 D P BRU 3 E BRU 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.605 ? 
covale ? covale4 D O3' BRU 3 E BRU 4 1_555 D P DU 4 E DU 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.609 ? 
#
_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 384 n n 
C1 C2 GOL sing 385 n n 
C1 H11 GOL sing 386 n n 
C1 H12 GOL sing 387 n n 
O1 HO1 GOL sing 388 n n 
C2 O2 GOL sing 389 n n 
C2 C3 GOL sing 390 n n 
C2 H2 GOL sing 391 n n 
O2 HO2 GOL sing 392 n n 
C3 O3 GOL sing 393 n n 
C3 H31 GOL sing 394 n n 
C3 H32 GOL sing 395 n n 
O3 HO3 GOL sing 396 n n 
#
_atom_sites.entry_id                     3VAG 
_atom_sites.fract_transf_matrix[1][1]    0.005994 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004252 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.026667 
_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]    0.012148 
_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 3 DIO A 1 401 6 DIO DIO . 
F 3 DIO A 1 402 8 DIO DIO . 
G 3 DIO A 1 403 9 DIO DIO . 
H 4 SO4 A 1 404 5 SO4 SO4 . 
I 4 SO4 A 1 405 7 SO4 SO4 . 
J 4 SO4 A 1 406 8 SO4 SO4 . 
K 4 SO4 A 1 407 11 SO4 SO4 . 
L 5 GOL A 1 408 1 GOL GOL . 
M 3 DIO B 1 401 1 DIO DIO . 
N 3 DIO B 1 402 4 DIO DIO . 
O 3 DIO B 1 403 7 DIO DIO . 
P 6 CPQ B 1 404 101 CPQ CPQ . 
Q 4 SO4 B 1 405 1 SO4 SO4 . 
R 4 SO4 B 1 406 6 SO4 SO4 . 
S 4 SO4 B 1 407 9 SO4 SO4 . 
T 5 GOL B 1 408 2 GOL GOL . 
U 7 HOH A 1 501 1 HOH HOH . 
U 7 HOH A 2 502 2 HOH HOH . 
U 7 HOH A 3 503 7 HOH HOH . 
U 7 HOH A 4 504 9 HOH HOH . 
U 7 HOH A 5 505 10 HOH HOH . 
U 7 HOH A 6 506 11 HOH HOH . 
U 7 HOH A 7 507 14 HOH HOH . 
U 7 HOH A 8 508 15 HOH HOH . 
U 7 HOH A 9 509 16 HOH HOH . 
U 7 HOH A 10 510 20 HOH HOH . 
U 7 HOH A 11 511 22 HOH HOH . 
U 7 HOH A 12 512 26 HOH HOH . 
U 7 HOH A 13 513 27 HOH HOH . 
U 7 HOH A 14 514 34 HOH HOH . 
U 7 HOH A 15 515 39 HOH HOH . 
U 7 HOH A 16 516 40 HOH HOH . 
U 7 HOH A 17 517 41 HOH HOH . 
U 7 HOH A 18 518 43 HOH HOH . 
U 7 HOH A 19 519 45 HOH HOH . 
U 7 HOH A 20 520 53 HOH HOH . 
U 7 HOH A 21 521 54 HOH HOH . 
U 7 HOH A 22 522 55 HOH HOH . 
U 7 HOH A 23 523 57 HOH HOH . 
U 7 HOH A 24 524 58 HOH HOH . 
U 7 HOH A 25 525 60 HOH HOH . 
U 7 HOH A 26 526 61 HOH HOH . 
U 7 HOH A 27 527 65 HOH HOH . 
U 7 HOH A 28 528 67 HOH HOH . 
U 7 HOH A 29 529 68 HOH HOH . 
U 7 HOH A 30 530 69 HOH HOH . 
U 7 HOH A 31 531 70 HOH HOH . 
U 7 HOH A 32 532 72 HOH HOH . 
U 7 HOH A 33 533 76 HOH HOH . 
U 7 HOH A 34 534 77 HOH HOH . 
U 7 HOH A 35 535 78 HOH HOH . 
U 7 HOH A 36 536 79 HOH HOH . 
U 7 HOH A 37 537 80 HOH HOH . 
U 7 HOH A 38 538 83 HOH HOH . 
U 7 HOH A 39 539 88 HOH HOH . 
U 7 HOH A 40 540 91 HOH HOH . 
U 7 HOH A 41 541 92 HOH HOH . 
U 7 HOH A 42 542 93 HOH HOH . 
U 7 HOH A 43 543 94 HOH HOH . 
U 7 HOH A 44 544 95 HOH HOH . 
U 7 HOH A 45 545 96 HOH HOH . 
U 7 HOH A 46 546 98 HOH HOH . 
U 7 HOH A 47 547 99 HOH HOH . 
U 7 HOH A 48 548 101 HOH HOH . 
U 7 HOH A 49 549 104 HOH HOH . 
U 7 HOH A 50 550 105 HOH HOH . 
U 7 HOH A 51 551 106 HOH HOH . 
U 7 HOH A 52 552 108 HOH HOH . 
U 7 HOH A 53 553 111 HOH HOH . 
U 7 HOH A 54 554 115 HOH HOH . 
U 7 HOH A 55 555 116 HOH HOH . 
U 7 HOH A 56 556 122 HOH HOH . 
U 7 HOH A 57 557 124 HOH HOH . 
U 7 HOH A 58 558 126 HOH HOH . 
U 7 HOH A 59 559 128 HOH HOH . 
U 7 HOH A 60 560 130 HOH HOH . 
U 7 HOH A 61 561 133 HOH HOH . 
U 7 HOH A 62 562 137 HOH HOH . 
U 7 HOH A 63 563 138 HOH HOH . 
U 7 HOH A 64 564 139 HOH HOH . 
U 7 HOH A 65 565 141 HOH HOH . 
U 7 HOH A 66 566 145 HOH HOH . 
U 7 HOH A 67 567 146 HOH HOH . 
U 7 HOH A 68 568 147 HOH HOH . 
U 7 HOH A 69 569 148 HOH HOH . 
U 7 HOH A 70 570 149 HOH HOH . 
U 7 HOH A 71 571 150 HOH HOH . 
U 7 HOH A 72 572 49 HOH HOH . 
V 7 HOH B 1 501 5 HOH HOH . 
V 7 HOH B 2 502 6 HOH HOH . 
V 7 HOH B 3 503 8 HOH HOH . 
V 7 HOH B 4 504 12 HOH HOH . 
V 7 HOH B 5 505 17 HOH HOH . 
V 7 HOH B 6 506 18 HOH HOH . 
V 7 HOH B 7 507 19 HOH HOH . 
V 7 HOH B 8 508 21 HOH HOH . 
V 7 HOH B 9 509 23 HOH HOH . 
V 7 HOH B 10 510 24 HOH HOH . 
V 7 HOH B 11 511 25 HOH HOH . 
V 7 HOH B 12 512 28 HOH HOH . 
V 7 HOH B 13 513 29 HOH HOH . 
V 7 HOH B 14 514 30 HOH HOH . 
V 7 HOH B 15 515 31 HOH HOH . 
V 7 HOH B 16 516 32 HOH HOH . 
V 7 HOH B 17 517 33 HOH HOH . 
V 7 HOH B 18 518 35 HOH HOH . 
V 7 HOH B 19 519 36 HOH HOH . 
V 7 HOH B 20 520 42 HOH HOH . 
V 7 HOH B 21 521 48 HOH HOH . 
V 7 HOH B 22 522 51 HOH HOH . 
V 7 HOH B 23 523 52 HOH HOH . 
V 7 HOH B 24 524 56 HOH HOH . 
V 7 HOH B 25 525 62 HOH HOH . 
V 7 HOH B 26 526 63 HOH HOH . 
V 7 HOH B 27 527 66 HOH HOH . 
V 7 HOH B 28 528 71 HOH HOH . 
V 7 HOH B 29 529 73 HOH HOH . 
V 7 HOH B 30 530 75 HOH HOH . 
V 7 HOH B 31 531 81 HOH HOH . 
V 7 HOH B 32 532 82 HOH HOH . 
V 7 HOH B 33 533 84 HOH HOH . 
V 7 HOH B 34 534 85 HOH HOH . 
V 7 HOH B 35 535 86 HOH HOH . 
V 7 HOH B 36 536 89 HOH HOH . 
V 7 HOH B 37 537 97 HOH HOH . 
V 7 HOH B 38 538 102 HOH HOH . 
V 7 HOH B 39 539 107 HOH HOH . 
V 7 HOH B 40 540 110 HOH HOH . 
V 7 HOH B 41 541 112 HOH HOH . 
V 7 HOH B 42 542 113 HOH HOH . 
V 7 HOH B 43 543 117 HOH HOH . 
V 7 HOH B 44 544 118 HOH HOH . 
V 7 HOH B 45 545 119 HOH HOH . 
V 7 HOH B 46 546 121 HOH HOH . 
V 7 HOH B 47 547 127 HOH HOH . 
V 7 HOH B 48 548 129 HOH HOH . 
V 7 HOH B 49 549 131 HOH HOH . 
V 7 HOH B 50 550 132 HOH HOH . 
V 7 HOH B 51 551 134 HOH HOH . 
V 7 HOH B 52 552 136 HOH HOH . 
V 7 HOH B 53 553 140 HOH HOH . 
V 7 HOH B 54 554 142 HOH HOH . 
V 7 HOH B 55 555 143 HOH HOH . 
V 7 HOH B 56 556 144 HOH HOH . 
V 7 HOH B 57 557 151 HOH HOH . 
V 7 HOH B 58 558 152 HOH HOH . 
V 7 HOH B 59 559 153 HOH HOH . 
V 7 HOH B 60 560 154 HOH HOH . 
V 7 HOH B 61 561 155 HOH HOH . 
V 7 HOH B 62 562 156 HOH HOH . 
W 7 HOH P 1 101 3 HOH HOH . 
W 7 HOH P 2 102 4 HOH HOH . 
W 7 HOH P 3 103 13 HOH HOH . 
W 7 HOH P 4 104 38 HOH HOH . 
W 7 HOH P 5 105 47 HOH HOH . 
W 7 HOH P 6 106 50 HOH HOH . 
W 7 HOH P 7 107 100 HOH HOH . 
W 7 HOH P 8 108 109 HOH HOH . 
W 7 HOH P 9 109 114 HOH HOH . 
W 7 HOH P 10 110 120 HOH HOH . 
W 7 HOH P 11 111 123 HOH HOH . 
W 7 HOH P 12 112 125 HOH HOH . 
W 7 HOH P 13 113 135 HOH HOH . 
X 7 HOH E 1 101 37 HOH HOH . 
X 7 HOH E 2 102 44 HOH HOH . 
X 7 HOH E 3 103 46 HOH HOH . 
X 7 HOH E 4 104 59 HOH HOH . 
X 7 HOH E 5 105 64 HOH HOH . 
X 7 HOH E 6 106 74 HOH HOH . 
X 7 HOH E 7 107 87 HOH HOH . 
X 7 HOH E 8 108 90 HOH HOH . 
X 7 HOH E 9 109 103 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 . . . L 5 -1.922 -22.503 15.902 1 75.37 ? C1 GOL 408 A 1 
HETATM 2 O O1 GOL . . . L 5 -3.213 -22.642 16.456 1 75.47 ? O1 GOL 408 A 1 
HETATM 3 C C2 GOL . . . L 5 -0.892 -22.343 17.016 1 75.33 ? C2 GOL 408 A 1 
HETATM 4 O O2 GOL . . . L 5 0.091 -21.42 16.616 1 75.17 ? O2 GOL 408 A 1 
HETATM 5 C C3 GOL . . . L 5 -0.234 -23.673 17.373 1 75.54 ? C3 GOL 408 A 1 
HETATM 6 O O3 GOL . . . L 5 -0.002 -23.724 18.763 1 75.55 ? O3 GOL 408 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           360 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           6 
#