data_5V60
#
_model_server_result.job_id            Qi94tK33GfzZqQKPMRiH3g 
_model_server_result.datetime_utc      '2024-11-14 19:33:15' 
_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          5v60 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":405}' 
#
_entry.id    5V60 
#
_exptl.entry_id    5V60 
_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    6 
_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            5V60 
_cell.length_a            41.757 
_cell.length_b            78.516 
_cell.length_c            152.566 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5V60 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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 
? 3 H 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 C LEU 180 A LEU 184 1_555 A N TPO 181 A TPO 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale2 A C TPO 181 A TPO 185 1_555 A N GLU 182 A GLU 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale3 A C GLU 182 A GLU 186 1_555 A N PTR 183 A PTR 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale4 A C PTR 183 A PTR 187 1_555 A N VAL 184 A VAL 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
metalc ? metalc1 A OD1 ASN 150 A ASN 154 1_555 I MG MG . A MG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? 
metalc ? metalc2 A OD2 ASP 163 A ASP 167 1_555 I MG MG . A MG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? 
metalc ? metalc3 A OD1 ASP 163 A ASP 167 1_555 J MG MG . A MG 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? 
metalc ? metalc4 A OD2 ASP 163 A ASP 167 1_555 J MG MG . A MG 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? 
metalc ? metalc5 B O2G ACP . A ACP 401 1_555 I MG MG . A MG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? 
metalc ? metalc6 B O2A ACP . A ACP 401 1_555 I MG MG . A MG 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? 
metalc ? metalc7 B O1G ACP . A ACP 401 1_555 J MG MG . A MG 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? 
metalc ? metalc8 B O2G ACP . A ACP 401 1_555 J MG MG . A MG 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? 
metalc ? metalc9 B O2B ACP . A ACP 401 1_555 J MG MG . A MG 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? 
metalc ? metalc10 I MG MG . A MG 408 1_555 K O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? 
metalc ? metalc11 I MG MG . A MG 408 1_555 K O HOH . A HOH 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc12 J MG MG . A MG 409 1_555 K O HOH . A HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc13 J MG MG . A MG 409 1_555 K O HOH . A HOH 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? 
#
_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 180 n n 
C1 C2 GOL sing 181 n n 
C1 H11 GOL sing 182 n n 
C1 H12 GOL sing 183 n n 
O1 HO1 GOL sing 184 n n 
C2 O2 GOL sing 185 n n 
C2 C3 GOL sing 186 n n 
C2 H2 GOL sing 187 n n 
O2 HO2 GOL sing 188 n n 
C3 O3 GOL sing 189 n n 
C3 H31 GOL sing 190 n n 
C3 H32 GOL sing 191 n n 
O3 HO3 GOL sing 192 n n 
#
_atom_sites.entry_id                     5V60 
_atom_sites.fract_transf_matrix[1][1]    0.023948 
_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]    0.012736 
_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]    0.006555 
_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 ACP A 1 401 1 ACP ACP . 
C 3 GOL A 1 402 1 GOL GOL . 
D 3 GOL A 1 403 2 GOL GOL . 
E 3 GOL A 1 404 3 GOL GOL . 
F 3 GOL A 1 405 4 GOL GOL . 
G 3 GOL A 1 406 5 GOL GOL . 
H 3 GOL A 1 407 6 GOL GOL . 
I 4 MG A 1 408 1 MG MG . 
J 4 MG A 1 409 2 MG MG . 
K 5 HOH A 1 501 168 HOH HOH . 
K 5 HOH A 2 502 173 HOH HOH . 
K 5 HOH A 3 503 162 HOH HOH . 
K 5 HOH A 4 504 123 HOH HOH . 
K 5 HOH A 5 505 118 HOH HOH . 
K 5 HOH A 6 506 29 HOH HOH . 
K 5 HOH A 7 507 164 HOH HOH . 
K 5 HOH A 8 508 172 HOH HOH . 
K 5 HOH A 9 509 128 HOH HOH . 
K 5 HOH A 10 510 15 HOH HOH . 
K 5 HOH A 11 511 12 HOH HOH . 
K 5 HOH A 12 512 13 HOH HOH . 
K 5 HOH A 13 513 174 HOH HOH . 
K 5 HOH A 14 514 42 HOH HOH . 
K 5 HOH A 15 515 132 HOH HOH . 
K 5 HOH A 16 516 17 HOH HOH . 
K 5 HOH A 17 517 49 HOH HOH . 
K 5 HOH A 18 518 142 HOH HOH . 
K 5 HOH A 19 519 129 HOH HOH . 
K 5 HOH A 20 520 130 HOH HOH . 
K 5 HOH A 21 521 122 HOH HOH . 
K 5 HOH A 22 522 24 HOH HOH . 
K 5 HOH A 23 523 8 HOH HOH . 
K 5 HOH A 24 524 10 HOH HOH . 
K 5 HOH A 25 525 131 HOH HOH . 
K 5 HOH A 26 526 45 HOH HOH . 
K 5 HOH A 27 527 149 HOH HOH . 
K 5 HOH A 28 528 65 HOH HOH . 
K 5 HOH A 29 529 59 HOH HOH . 
K 5 HOH A 30 530 14 HOH HOH . 
K 5 HOH A 31 531 146 HOH HOH . 
K 5 HOH A 32 532 126 HOH HOH . 
K 5 HOH A 33 533 145 HOH HOH . 
K 5 HOH A 34 534 22 HOH HOH . 
K 5 HOH A 35 535 18 HOH HOH . 
K 5 HOH A 36 536 166 HOH HOH . 
K 5 HOH A 37 537 156 HOH HOH . 
K 5 HOH A 38 538 160 HOH HOH . 
K 5 HOH A 39 539 51 HOH HOH . 
K 5 HOH A 40 540 27 HOH HOH . 
K 5 HOH A 41 541 66 HOH HOH . 
K 5 HOH A 42 542 30 HOH HOH . 
K 5 HOH A 43 543 139 HOH HOH . 
K 5 HOH A 44 544 127 HOH HOH . 
K 5 HOH A 45 545 16 HOH HOH . 
K 5 HOH A 46 546 140 HOH HOH . 
K 5 HOH A 47 547 136 HOH HOH . 
K 5 HOH A 48 548 144 HOH HOH . 
K 5 HOH A 49 549 58 HOH HOH . 
K 5 HOH A 50 550 167 HOH HOH . 
K 5 HOH A 51 551 137 HOH HOH . 
K 5 HOH A 52 552 170 HOH HOH . 
K 5 HOH A 53 553 2 HOH HOH . 
K 5 HOH A 54 554 81 HOH HOH . 
K 5 HOH A 55 555 158 HOH HOH . 
K 5 HOH A 56 556 157 HOH HOH . 
K 5 HOH A 57 557 135 HOH HOH . 
K 5 HOH A 58 558 150 HOH HOH . 
K 5 HOH A 59 559 92 HOH HOH . 
K 5 HOH A 60 560 161 HOH HOH . 
K 5 HOH A 61 561 35 HOH HOH . 
K 5 HOH A 62 562 124 HOH HOH . 
K 5 HOH A 63 563 125 HOH HOH . 
K 5 HOH A 64 564 4 HOH HOH . 
K 5 HOH A 65 565 171 HOH HOH . 
K 5 HOH A 66 566 133 HOH HOH . 
K 5 HOH A 67 567 120 HOH HOH . 
K 5 HOH A 68 568 6 HOH HOH . 
K 5 HOH A 69 569 121 HOH HOH . 
K 5 HOH A 70 570 119 HOH HOH . 
K 5 HOH A 71 571 159 HOH HOH . 
K 5 HOH A 72 572 90 HOH HOH . 
K 5 HOH A 73 573 165 HOH HOH . 
K 5 HOH A 74 574 163 HOH HOH . 
K 5 HOH A 75 575 155 HOH HOH . 
K 5 HOH A 76 576 28 HOH HOH . 
K 5 HOH A 77 577 134 HOH HOH . 
K 5 HOH A 78 578 138 HOH HOH . 
K 5 HOH A 79 579 154 HOH HOH . 
K 5 HOH A 80 580 141 HOH HOH . 
K 5 HOH A 81 581 148 HOH HOH . 
K 5 HOH A 82 582 143 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 . . . F 3 -8.937 0.447 32.447 1 84.52 ? C1 GOL 405 A 1 
HETATM 2 O O1 GOL . . . F 3 -9.044 -0.731 31.639 1 84.25 ? O1 GOL 405 A 1 
HETATM 3 C C2 GOL . . . F 3 -9.15 1.685 31.583 1 85.25 ? C2 GOL 405 A 1 
HETATM 4 O O2 GOL . . . F 3 -9.431 2.805 32.432 1 83.08 ? O2 GOL 405 A 1 
HETATM 5 C C3 GOL . . . F 3 -7.925 1.95 30.694 1 85.49 ? C3 GOL 405 A 1 
HETATM 6 O O3 GOL . . . F 3 -7.189 3.102 31.131 1 83.52 ? O3 GOL 405 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           232 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           6 
#