data_4Q8F
#
_model_server_result.job_id            1g5O-ZBOonyKsS0uUeV_OA 
_model_server_result.datetime_utc      '2024-11-25 12:29:17' 
_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          4q8f 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":505}' 
#
_entry.id    4Q8F 
#
_exptl.entry_id    4Q8F 
_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    3 
_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         120 
_cell.entry_id            4Q8F 
_cell.length_a            98.692 
_cell.length_b            98.692 
_cell.length_c            81.812 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4Q8F 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        169 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_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 G N N 
? 6 H 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
covale ? covale1 B O3' DC 3 T DC 4 1_555 B P P9G 4 T P9G 5 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.614 ? 
covale ? covale2 B O3' DC 3 T DC 4 1_555 B P P9G 4 T P9G 5 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.609 ? 
covale ? covale3 B O3' P9G 4 T P9G 5 1_555 B P DT 5 T DT 6 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.603 ? 
metalc ? metalc1 A OD1 ASP 16 A ASP 13 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? 
metalc ? metalc2 A OD2 ASP 16 A ASP 13 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.867 ? 
metalc ? metalc3 A OD2 ASP 16 A ASP 13 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? 
metalc ? metalc4 A O MET 17 A MET 14 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? 
metalc ? metalc5 A OD2 ASP 118 A ASP 115 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
metalc ? metalc6 A OD1 ASP 118 A ASP 115 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
metalc ? metalc7 A OE2 GLU 119 A GLU 116 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? 
metalc ? metalc8 D MG MG . A MG 501 1_555 F O1B XG4 . A XG4 503 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.053 ? 
metalc ? metalc9 D MG MG . A MG 501 1_555 F O1B XG4 . A XG4 503 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.151 ? 
metalc ? metalc10 D MG MG . A MG 501 1_555 F O1A XG4 . A XG4 503 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.228 ? 
metalc ? metalc11 D MG MG . A MG 501 1_555 F O1G XG4 . A XG4 503 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.242 ? 
metalc ? metalc12 D MG MG . A MG 501 1_555 F O1G XG4 . A XG4 503 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.252 ? 
metalc ? metalc13 D MG MG . A MG 501 1_555 F O1A XG4 . A XG4 503 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.349 ? 
metalc ? metalc14 E MG MG . A MG 502 1_555 F O1A XG4 . A XG4 503 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.371 ? 
metalc ? metalc15 E MG MG . A MG 502 1_555 F O1A XG4 . A XG4 503 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.387 ? 
metalc ? metalc16 E MG MG . A MG 502 1_555 K O HOH . A HOH 615 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? 
metalc ? metalc17 E MG MG . A MG 502 1_555 C O3' DC 8 P DC 8 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.735 ? 
metalc ? metalc18 E MG MG . A MG 502 1_555 C O3' DC 8 P DC 8 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.775 ? 
hydrog WATSON-CRICK hydrog1 B N3 DT 5 T DT 6 1_555 C N1 DA 7 P DA 7 1_555 ? ? ? ? A ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 B O4 DT 5 T DT 6 1_555 C N6 DA 7 P DA 7 1_555 ? ? ? ? A ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 B N3 DC 6 T DC 7 1_555 C N1 DG 6 P DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 B N4 DC 6 T DC 7 1_555 C O6 DG 6 P DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 B O2 DC 6 T DC 7 1_555 C N2 DG 6 P DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 B N1 DA 7 T DA 8 1_555 C N3 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 B N6 DA 7 T DA 8 1_555 C O4 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 B N3 DC 8 T DC 9 1_555 C N1 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 B N4 DC 8 T DC 9 1_555 C O6 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 B O2 DC 8 T DC 9 1_555 C N2 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 B N1 DA 9 T DA 10 1_555 C N3 DT 3 P DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 B N6 DA 9 T DA 10 1_555 C O4 DT 3 P DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 B N3 DC 10 T DC 11 1_555 C N1 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog14 B N4 DC 10 T DC 11 1_555 C O6 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 B O2 DC 10 T DC 11 1_555 C N2 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog16 B N3 DT 11 T DT 12 1_555 C N1 DA 1 P DA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog17 B O4 DT 11 T DT 12 1_555 C N6 DA 1 P DA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_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 278 n n 
C1 C2 GOL sing 279 n n 
C1 H11 GOL sing 280 n n 
C1 H12 GOL sing 281 n n 
O1 HO1 GOL sing 282 n n 
C2 O2 GOL sing 283 n n 
C2 C3 GOL sing 284 n n 
C2 H2 GOL sing 285 n n 
O2 HO2 GOL sing 286 n n 
C3 O3 GOL sing 287 n n 
C3 H31 GOL sing 288 n n 
C3 H32 GOL sing 289 n n 
O3 HO3 GOL sing 290 n n 
#
_atom_sites.entry_id                     4Q8F 
_atom_sites.fract_transf_matrix[1][1]    0.010133 
_atom_sites.fract_transf_matrix[1][2]    0.00585 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.0117 
_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]    0.012223 
_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
D 4 MG A 1 501 433 MG MG . 
E 4 MG A 1 502 434 MG MG . 
F 5 XG4 A 1 503 435 XG4 XG4 . 
G 6 GOL A 1 504 503 GOL GOL . 
H 6 GOL A 1 505 504 GOL GOL . 
I 5 XG4 A 1 506 505 XG4 XG4 . 
J 6 GOL A 1 507 549 GOL GOL . 
K 7 HOH A 1 601 506 HOH HOH . 
K 7 HOH A 2 602 507 HOH HOH . 
K 7 HOH A 3 603 508 HOH HOH . 
K 7 HOH A 4 604 509 HOH HOH . 
K 7 HOH A 5 605 510 HOH HOH . 
K 7 HOH A 6 606 511 HOH HOH . 
K 7 HOH A 7 607 514 HOH HOH . 
K 7 HOH A 8 608 515 HOH HOH . 
K 7 HOH A 9 609 516 HOH HOH . 
K 7 HOH A 10 610 517 HOH HOH . 
K 7 HOH A 11 611 518 HOH HOH . 
K 7 HOH A 12 612 519 HOH HOH . 
K 7 HOH A 13 613 520 HOH HOH . 
K 7 HOH A 14 614 521 HOH HOH . 
K 7 HOH A 15 615 522 HOH HOH . 
K 7 HOH A 16 616 523 HOH HOH . 
K 7 HOH A 17 617 524 HOH HOH . 
K 7 HOH A 18 618 525 HOH HOH . 
K 7 HOH A 19 619 526 HOH HOH . 
K 7 HOH A 20 620 527 HOH HOH . 
K 7 HOH A 21 621 529 HOH HOH . 
K 7 HOH A 22 622 530 HOH HOH . 
K 7 HOH A 23 623 531 HOH HOH . 
K 7 HOH A 24 624 532 HOH HOH . 
K 7 HOH A 25 625 533 HOH HOH . 
K 7 HOH A 26 626 534 HOH HOH . 
K 7 HOH A 27 627 535 HOH HOH . 
K 7 HOH A 28 628 536 HOH HOH . 
K 7 HOH A 29 629 540 HOH HOH . 
K 7 HOH A 30 630 541 HOH HOH . 
K 7 HOH A 31 631 542 HOH HOH . 
K 7 HOH A 32 632 544 HOH HOH . 
K 7 HOH A 33 633 548 HOH HOH . 
L 7 HOH T 1 101 538 HOH HOH . 
L 7 HOH T 2 102 539 HOH HOH . 
L 7 HOH T 3 103 546 HOH HOH . 
L 7 HOH T 4 104 547 HOH HOH . 
M 7 HOH P 1 101 512 HOH HOH . 
M 7 HOH P 2 102 545 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 52.577 16.525 -5.461 1 34.83 ? C1 GOL 505 A 1 
HETATM 2 O O1 GOL . . . H 6 52.941 16.693 -4.109 1 31.56 ? O1 GOL 505 A 1 
HETATM 3 C C2 GOL . . . H 6 53.818 16.557 -6.349 1 40.36 ? C2 GOL 505 A 1 
HETATM 4 O O2 GOL . . . H 6 53.928 15.346 -7.064 1 31.19 ? O2 GOL 505 A 1 
HETATM 5 C C3 GOL . . . H 6 53.724 17.726 -7.323 1 41.66 ? C3 GOL 505 A 1 
HETATM 6 O O3 GOL . . . H 6 54.766 17.639 -8.27 1 45.72 ? O3 GOL 505 A 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           399 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           6 
#