data_8OIB
#
_model_server_result.job_id            b0juU7JxM3JfhvB79ygZjA 
_model_server_result.datetime_utc      '2024-11-23 23:35:43' 
_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          8oib 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":401}' 
#
_entry.id    8OIB 
#
_exptl.entry_id    8OIB 
_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    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90.562 
_cell.angle_gamma         90 
_cell.entry_id            8OIB 
_cell.length_a            51.034 
_cell.length_b            156.998 
_cell.length_c            88.729 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8OIB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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 
_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 H N N 
? 3 J N N 
? 3 L 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 OD1 ASP 10 A ASP 10 1_555 E CA CA . A CA 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? 
metalc ? metalc2 A OD1 ASP 15 A ASP 15 1_555 E CA CA . A CA 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? 
metalc ? metalc3 A OD2 ASP 15 A ASP 15 1_555 E CA CA . A CA 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? 
metalc ? metalc4 A O THR 142 A THR 142 1_555 E CA CA . A CA 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? 
metalc ? metalc5 A OD2 ASP 263 A ASP 263 1_555 E CA CA . A CA 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? 
metalc ? metalc6 E CA CA . A CA 400 1_555 F O3 GOL . A GOL 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? 
metalc ? metalc7 E CA CA . A CA 400 1_555 M O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? 
metalc ? metalc8 E CA CA . A CA 400 1_555 M O HOH . A HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? 
metalc ? metalc9 B OD1 ASP 10 B ASP 10 1_555 G CA CA . B CA 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? 
metalc ? metalc10 B OD1 ASP 15 B ASP 15 1_555 G CA CA . B CA 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? 
metalc ? metalc11 B OD2 ASP 15 B ASP 15 1_555 G CA CA . B CA 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? 
metalc ? metalc12 B O THR 142 B THR 142 1_555 G CA CA . B CA 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? 
metalc ? metalc13 B OD2 ASP 263 B ASP 263 1_555 G CA CA . B CA 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? 
metalc ? metalc14 G CA CA . B CA 400 1_555 H O3 GOL . B GOL 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? 
metalc ? metalc15 G CA CA . B CA 400 1_555 N O HOH . B HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? 
metalc ? metalc16 G CA CA . B CA 400 1_555 N O HOH . B HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? 
metalc ? metalc17 C OD1 ASP 10 C ASP 10 1_555 I CA CA . C CA 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? 
metalc ? metalc18 C OD1 ASP 15 C ASP 15 1_555 I CA CA . C CA 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? 
metalc ? metalc19 C OD2 ASP 15 C ASP 15 1_555 I CA CA . C CA 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? 
metalc ? metalc20 C O THR 142 C THR 142 1_555 I CA CA . C CA 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? 
metalc ? metalc21 C OD2 ASP 263 C ASP 263 1_555 I CA CA . C CA 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? 
metalc ? metalc22 I CA CA . C CA 400 1_555 J O3 GOL . C GOL 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? 
metalc ? metalc23 I CA CA . C CA 400 1_555 O O HOH . C HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? 
metalc ? metalc24 I CA CA . C CA 400 1_555 O O HOH . C HOH 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? 
metalc ? metalc25 D OD1 ASP 10 D ASP 10 1_555 K CA CA . D CA 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? 
metalc ? metalc26 D OD1 ASP 15 D ASP 15 1_555 K CA CA . D CA 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? 
metalc ? metalc27 D OD2 ASP 15 D ASP 15 1_555 K CA CA . D CA 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? 
metalc ? metalc28 D O THR 142 D THR 142 1_555 K CA CA . D CA 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? 
metalc ? metalc29 D OD2 ASP 263 D ASP 263 1_555 K CA CA . D CA 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? 
metalc ? metalc30 K CA CA . D CA 400 1_555 L O3 GOL . D GOL 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc31 K CA CA . D CA 400 1_555 P O HOH . D HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? 
metalc ? metalc32 K CA CA . D CA 400 1_555 P O HOH . D HOH 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? 
#
_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 129 n n 
C1 C2 GOL sing 130 n n 
C1 H11 GOL sing 131 n n 
C1 H12 GOL sing 132 n n 
O1 HO1 GOL sing 133 n n 
C2 O2 GOL sing 134 n n 
C2 C3 GOL sing 135 n n 
C2 H2 GOL sing 136 n n 
O2 HO2 GOL sing 137 n n 
C3 O3 GOL sing 138 n n 
C3 H31 GOL sing 139 n n 
C3 H32 GOL sing 140 n n 
O3 HO3 GOL sing 141 n n 
#
_atom_sites.entry_id                     8OIB 
_atom_sites.fract_transf_matrix[1][1]    0.019595 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000192 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00637 
_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]    0.011271 
_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 CA A 1 400 400 CA CA . 
F 3 GOL A 1 401 401 GOL GOL . 
G 2 CA B 1 400 400 CA CA . 
H 3 GOL B 1 401 401 GOL GOL . 
I 2 CA C 1 400 400 CA CA . 
J 3 GOL C 1 401 401 GOL GOL . 
K 2 CA D 1 400 400 CA CA . 
L 3 GOL D 1 401 401 GOL GOL . 
M 4 HOH A 1 501 102 HOH HOH . 
M 4 HOH A 2 502 6 HOH HOH . 
M 4 HOH A 3 503 107 HOH HOH . 
M 4 HOH A 4 504 92 HOH HOH . 
M 4 HOH A 5 505 105 HOH HOH . 
M 4 HOH A 6 506 82 HOH HOH . 
M 4 HOH A 7 507 3 HOH HOH . 
M 4 HOH A 8 508 4 HOH HOH . 
M 4 HOH A 9 509 1 HOH HOH . 
M 4 HOH A 10 510 38 HOH HOH . 
M 4 HOH A 11 511 103 HOH HOH . 
M 4 HOH A 12 512 77 HOH HOH . 
M 4 HOH A 13 513 87 HOH HOH . 
M 4 HOH A 14 514 47 HOH HOH . 
M 4 HOH A 15 515 79 HOH HOH . 
M 4 HOH A 16 516 100 HOH HOH . 
M 4 HOH A 17 517 104 HOH HOH . 
M 4 HOH A 18 518 40 HOH HOH . 
M 4 HOH A 19 519 35 HOH HOH . 
M 4 HOH A 20 520 20 HOH HOH . 
M 4 HOH A 21 521 106 HOH HOH . 
M 4 HOH A 22 522 26 HOH HOH . 
M 4 HOH A 23 523 46 HOH HOH . 
M 4 HOH A 24 524 90 HOH HOH . 
M 4 HOH A 25 525 68 HOH HOH . 
M 4 HOH A 26 526 96 HOH HOH . 
M 4 HOH A 27 527 67 HOH HOH . 
M 4 HOH A 28 528 71 HOH HOH . 
M 4 HOH A 29 529 17 HOH HOH . 
M 4 HOH A 30 530 8 HOH HOH . 
M 4 HOH A 31 531 76 HOH HOH . 
M 4 HOH A 32 532 86 HOH HOH . 
M 4 HOH A 33 533 93 HOH HOH . 
M 4 HOH A 34 534 88 HOH HOH . 
M 4 HOH A 35 535 5 HOH HOH . 
N 4 HOH B 1 501 19 HOH HOH . 
N 4 HOH B 2 502 16 HOH HOH . 
N 4 HOH B 3 503 23 HOH HOH . 
N 4 HOH B 4 504 110 HOH HOH . 
N 4 HOH B 5 505 78 HOH HOH . 
N 4 HOH B 6 506 125 HOH HOH . 
N 4 HOH B 7 507 108 HOH HOH . 
N 4 HOH B 8 508 109 HOH HOH . 
N 4 HOH B 9 509 13 HOH HOH . 
N 4 HOH B 10 510 45 HOH HOH . 
N 4 HOH B 11 511 42 HOH HOH . 
N 4 HOH B 12 512 28 HOH HOH . 
N 4 HOH B 13 513 14 HOH HOH . 
N 4 HOH B 14 514 25 HOH HOH . 
N 4 HOH B 15 515 7 HOH HOH . 
N 4 HOH B 16 516 83 HOH HOH . 
N 4 HOH B 17 517 34 HOH HOH . 
N 4 HOH B 18 518 10 HOH HOH . 
N 4 HOH B 19 519 36 HOH HOH . 
N 4 HOH B 20 520 66 HOH HOH . 
N 4 HOH B 21 521 9 HOH HOH . 
N 4 HOH B 22 522 75 HOH HOH . 
N 4 HOH B 23 523 111 HOH HOH . 
N 4 HOH B 24 524 18 HOH HOH . 
N 4 HOH B 25 525 89 HOH HOH . 
N 4 HOH B 26 526 99 HOH HOH . 
O 4 HOH C 1 501 15 HOH HOH . 
O 4 HOH C 2 502 112 HOH HOH . 
O 4 HOH C 3 503 115 HOH HOH . 
O 4 HOH C 4 504 84 HOH HOH . 
O 4 HOH C 5 505 43 HOH HOH . 
O 4 HOH C 6 506 39 HOH HOH . 
O 4 HOH C 7 507 80 HOH HOH . 
O 4 HOH C 8 508 48 HOH HOH . 
O 4 HOH C 9 509 114 HOH HOH . 
O 4 HOH C 10 510 33 HOH HOH . 
O 4 HOH C 11 511 52 HOH HOH . 
O 4 HOH C 12 512 51 HOH HOH . 
O 4 HOH C 13 513 24 HOH HOH . 
O 4 HOH C 14 514 61 HOH HOH . 
O 4 HOH C 15 515 97 HOH HOH . 
O 4 HOH C 16 516 55 HOH HOH . 
O 4 HOH C 17 517 117 HOH HOH . 
O 4 HOH C 18 518 49 HOH HOH . 
O 4 HOH C 19 519 101 HOH HOH . 
O 4 HOH C 20 520 32 HOH HOH . 
O 4 HOH C 21 521 37 HOH HOH . 
O 4 HOH C 22 522 30 HOH HOH . 
O 4 HOH C 23 523 50 HOH HOH . 
O 4 HOH C 24 524 116 HOH HOH . 
O 4 HOH C 25 525 113 HOH HOH . 
O 4 HOH C 26 526 11 HOH HOH . 
O 4 HOH C 27 527 62 HOH HOH . 
O 4 HOH C 28 528 63 HOH HOH . 
O 4 HOH C 29 529 59 HOH HOH . 
O 4 HOH C 30 530 54 HOH HOH . 
P 4 HOH D 1 501 74 HOH HOH . 
P 4 HOH D 2 502 122 HOH HOH . 
P 4 HOH D 3 503 120 HOH HOH . 
P 4 HOH D 4 504 53 HOH HOH . 
P 4 HOH D 5 505 123 HOH HOH . 
P 4 HOH D 6 506 81 HOH HOH . 
P 4 HOH D 7 507 126 HOH HOH . 
P 4 HOH D 8 508 41 HOH HOH . 
P 4 HOH D 9 509 94 HOH HOH . 
P 4 HOH D 10 510 85 HOH HOH . 
P 4 HOH D 11 511 12 HOH HOH . 
P 4 HOH D 12 512 124 HOH HOH . 
P 4 HOH D 13 513 31 HOH HOH . 
P 4 HOH D 14 514 22 HOH HOH . 
P 4 HOH D 15 515 70 HOH HOH . 
P 4 HOH D 16 516 98 HOH HOH . 
P 4 HOH D 17 517 21 HOH HOH . 
P 4 HOH D 18 518 95 HOH HOH . 
P 4 HOH D 19 519 69 HOH HOH . 
P 4 HOH D 20 520 57 HOH HOH . 
P 4 HOH D 21 521 73 HOH HOH . 
P 4 HOH D 22 522 27 HOH HOH . 
P 4 HOH D 23 523 65 HOH HOH . 
P 4 HOH D 24 524 119 HOH HOH . 
P 4 HOH D 25 525 58 HOH HOH . 
P 4 HOH D 26 526 29 HOH HOH . 
P 4 HOH D 27 527 56 HOH HOH . 
P 4 HOH D 28 528 64 HOH HOH . 
P 4 HOH D 29 529 121 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 . . . J 3 10.053 2.488 41.248 1 56.1 0 C1 GOL 401 C 1 
HETATM 2 O O1 GOL . . . J 3 9.367 2.003 40.098 1 53.93 0 O1 GOL 401 C 1 
HETATM 3 C C2 GOL . . . J 3 9.558 1.79 42.495 1 58.78 0 C2 GOL 401 C 1 
HETATM 4 O O2 GOL . . . J 3 10.031 0.442 42.557 1 68.94 0 O2 GOL 401 C 1 
HETATM 5 C C3 GOL . . . J 3 9.95 2.479 43.775 1 57.11 0 C3 GOL 401 C 1 
HETATM 6 O O3 GOL . . . J 3 9.501 1.701 44.881 1 56.65 0 O3 GOL 401 C 1 
#
_model_server_stats.io_time_ms              35 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           250 
_model_server_stats.encode_time_ms          14 
_model_server_stats.element_count           6 
#