data_8VMF
#
_model_server_result.job_id            R7s2dEcNvkohQ3Bqp-s0vQ 
_model_server_result.datetime_utc      '2024-11-28 22:14:39' 
_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          8vmf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":507}' 
#
_entry.id    8VMF 
#
_exptl.entry_id    8VMF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          7 
_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            8VMF 
_cell.length_a            82.251 
_cell.length_b            82.251 
_cell.length_c            280.354 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8VMF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    'P 61 2 (x,y,z+5/12)' 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
_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
? 7 H N N 
? 7 I N N 
? 7 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 OD1 ASN 161 A ASN 186 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? 
metalc ? metalc2 A OD2 ASP 175 A ASP 200 1_555 D MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? 
metalc ? metalc3 A OD1 ASP 175 A ASP 200 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.626 ? 
metalc ? metalc4 D MG MG . A MG 501 1_555 G O1B ADP . A ADP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? 
metalc ? metalc5 D MG MG . A MG 501 1_555 L O HOH . A HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.907 ? 
metalc ? metalc6 E MG MG . A MG 502 1_555 G O3B ADP . A ADP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? 
metalc ? metalc7 E MG MG . A MG 502 1_555 L O HOH . A HOH 647 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? 
#
_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 176 n n 
C1 C2 GOL sing 177 n n 
C1 H11 GOL sing 178 n n 
C1 H12 GOL sing 179 n n 
O1 HO1 GOL sing 180 n n 
C2 O2 GOL sing 181 n n 
C2 C3 GOL sing 182 n n 
C2 H2 GOL sing 183 n n 
O2 HO2 GOL sing 184 n n 
C3 O3 GOL sing 185 n n 
C3 H31 GOL sing 186 n n 
C3 H32 GOL sing 187 n n 
O3 HO3 GOL sing 188 n n 
#
_atom_sites.entry_id                     8VMF 
_atom_sites.fract_transf_matrix[1][1]    0.012158 
_atom_sites.fract_transf_matrix[1][2]    0.007019 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014039 
_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]    0.003567 
_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 1 501 501 MG MG . 
E 4 MG A 1 502 502 MG MG . 
F 5 AF3 A 1 503 601 AF3 AF3 . 
G 6 ADP A 1 504 1 ADP ADP . 
H 7 GOL A 1 505 1 GOL GOL . 
I 7 GOL A 1 506 2 GOL GOL . 
J 7 GOL A 1 507 3 GOL GOL . 
K 8 CL A 1 508 1 CL CL . 
L 9 HOH A 1 601 120 HOH HOH . 
L 9 HOH A 2 602 119 HOH HOH . 
L 9 HOH A 3 603 38 HOH HOH . 
L 9 HOH A 4 604 165 HOH HOH . 
L 9 HOH A 5 605 123 HOH HOH . 
L 9 HOH A 6 606 144 HOH HOH . 
L 9 HOH A 7 607 162 HOH HOH . 
L 9 HOH A 8 608 167 HOH HOH . 
L 9 HOH A 9 609 160 HOH HOH . 
L 9 HOH A 10 610 82 HOH HOH . 
L 9 HOH A 11 611 153 HOH HOH . 
L 9 HOH A 12 612 86 HOH HOH . 
L 9 HOH A 13 613 37 HOH HOH . 
L 9 HOH A 14 614 58 HOH HOH . 
L 9 HOH A 15 615 35 HOH HOH . 
L 9 HOH A 16 616 81 HOH HOH . 
L 9 HOH A 17 617 135 HOH HOH . 
L 9 HOH A 18 618 142 HOH HOH . 
L 9 HOH A 19 619 158 HOH HOH . 
L 9 HOH A 20 620 21 HOH HOH . 
L 9 HOH A 21 621 51 HOH HOH . 
L 9 HOH A 22 622 161 HOH HOH . 
L 9 HOH A 23 623 19 HOH HOH . 
L 9 HOH A 24 624 166 HOH HOH . 
L 9 HOH A 25 625 107 HOH HOH . 
L 9 HOH A 26 626 77 HOH HOH . 
L 9 HOH A 27 627 133 HOH HOH . 
L 9 HOH A 28 628 25 HOH HOH . 
L 9 HOH A 29 629 3 HOH HOH . 
L 9 HOH A 30 630 96 HOH HOH . 
L 9 HOH A 31 631 117 HOH HOH . 
L 9 HOH A 32 632 61 HOH HOH . 
L 9 HOH A 33 633 66 HOH HOH . 
L 9 HOH A 34 634 18 HOH HOH . 
L 9 HOH A 35 635 164 HOH HOH . 
L 9 HOH A 36 636 70 HOH HOH . 
L 9 HOH A 37 637 15 HOH HOH . 
L 9 HOH A 38 638 68 HOH HOH . 
L 9 HOH A 39 639 141 HOH HOH . 
L 9 HOH A 40 640 126 HOH HOH . 
L 9 HOH A 41 641 44 HOH HOH . 
L 9 HOH A 42 642 22 HOH HOH . 
L 9 HOH A 43 643 69 HOH HOH . 
L 9 HOH A 44 644 159 HOH HOH . 
L 9 HOH A 45 645 131 HOH HOH . 
L 9 HOH A 46 646 163 HOH HOH . 
L 9 HOH A 47 647 129 HOH HOH . 
L 9 HOH A 48 648 5 HOH HOH . 
L 9 HOH A 49 649 14 HOH HOH . 
L 9 HOH A 50 650 102 HOH HOH . 
L 9 HOH A 51 651 17 HOH HOH . 
L 9 HOH A 52 652 168 HOH HOH . 
L 9 HOH A 53 653 13 HOH HOH . 
L 9 HOH A 54 654 97 HOH HOH . 
L 9 HOH A 55 655 46 HOH HOH . 
L 9 HOH A 56 656 26 HOH HOH . 
L 9 HOH A 57 657 31 HOH HOH . 
L 9 HOH A 58 658 95 HOH HOH . 
L 9 HOH A 59 659 62 HOH HOH . 
L 9 HOH A 60 660 152 HOH HOH . 
L 9 HOH A 61 661 4 HOH HOH . 
L 9 HOH A 62 662 10 HOH HOH . 
L 9 HOH A 63 663 73 HOH HOH . 
L 9 HOH A 64 664 57 HOH HOH . 
L 9 HOH A 65 665 88 HOH HOH . 
L 9 HOH A 66 666 169 HOH HOH . 
L 9 HOH A 67 667 8 HOH HOH . 
L 9 HOH A 68 668 23 HOH HOH . 
L 9 HOH A 69 669 56 HOH HOH . 
L 9 HOH A 70 670 6 HOH HOH . 
L 9 HOH A 71 671 9 HOH HOH . 
L 9 HOH A 72 672 138 HOH HOH . 
L 9 HOH A 73 673 49 HOH HOH . 
L 9 HOH A 74 674 34 HOH HOH . 
L 9 HOH A 75 675 12 HOH HOH . 
L 9 HOH A 76 676 24 HOH HOH . 
L 9 HOH A 77 677 2 HOH HOH . 
L 9 HOH A 78 678 125 HOH HOH . 
L 9 HOH A 79 679 92 HOH HOH . 
L 9 HOH A 80 680 16 HOH HOH . 
L 9 HOH A 81 681 83 HOH HOH . 
L 9 HOH A 82 682 1 HOH HOH . 
L 9 HOH A 83 683 122 HOH HOH . 
L 9 HOH A 84 684 63 HOH HOH . 
L 9 HOH A 85 685 124 HOH HOH . 
L 9 HOH A 86 686 7 HOH HOH . 
L 9 HOH A 87 687 40 HOH HOH . 
L 9 HOH A 88 688 106 HOH HOH . 
L 9 HOH A 89 689 150 HOH HOH . 
L 9 HOH A 90 690 116 HOH HOH . 
L 9 HOH A 91 691 84 HOH HOH . 
L 9 HOH A 92 692 76 HOH HOH . 
L 9 HOH A 93 693 59 HOH HOH . 
L 9 HOH A 94 694 121 HOH HOH . 
L 9 HOH A 95 695 157 HOH HOH . 
L 9 HOH A 96 696 101 HOH HOH . 
L 9 HOH A 97 697 50 HOH HOH . 
L 9 HOH A 98 698 65 HOH HOH . 
L 9 HOH A 99 699 33 HOH HOH . 
L 9 HOH A 100 700 105 HOH HOH . 
L 9 HOH A 101 701 154 HOH HOH . 
L 9 HOH A 102 702 74 HOH HOH . 
L 9 HOH A 103 703 149 HOH HOH . 
L 9 HOH A 104 704 115 HOH HOH . 
L 9 HOH A 105 705 155 HOH HOH . 
L 9 HOH A 106 706 98 HOH HOH . 
L 9 HOH A 107 707 127 HOH HOH . 
L 9 HOH A 108 708 45 HOH HOH . 
L 9 HOH A 109 709 118 HOH HOH . 
L 9 HOH A 110 710 139 HOH HOH . 
L 9 HOH A 111 711 113 HOH HOH . 
L 9 HOH A 112 712 85 HOH HOH . 
L 9 HOH A 113 713 104 HOH HOH . 
L 9 HOH A 114 714 93 HOH HOH . 
L 9 HOH A 115 715 103 HOH HOH . 
L 9 HOH A 116 716 134 HOH HOH . 
L 9 HOH A 117 717 11 HOH HOH . 
L 9 HOH A 118 718 55 HOH HOH . 
L 9 HOH A 119 719 136 HOH HOH . 
L 9 HOH A 120 720 112 HOH HOH . 
L 9 HOH A 121 721 109 HOH HOH . 
L 9 HOH A 122 722 137 HOH HOH . 
M 9 HOH B 1 501 27 HOH HOH . 
M 9 HOH B 2 502 78 HOH HOH . 
M 9 HOH B 3 503 128 HOH HOH . 
M 9 HOH B 4 504 29 HOH HOH . 
M 9 HOH B 5 505 47 HOH HOH . 
M 9 HOH B 6 506 20 HOH HOH . 
M 9 HOH B 7 507 91 HOH HOH . 
M 9 HOH B 8 508 156 HOH HOH . 
M 9 HOH B 9 509 48 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 7 -7.834 -37.242 -28.331 1 67.74 ? C1 GOL 507 A 1 
HETATM 2 O O1 GOL . . . J 7 -7.832 -38.651 -28.209 1 60.75 ? O1 GOL 507 A 1 
HETATM 3 C C2 GOL . . . J 7 -8.485 -36.898 -29.676 1 72.27 ? C2 GOL 507 A 1 
HETATM 4 O O2 GOL . . . J 7 -9.656 -36.125 -29.521 1 66.69 ? O2 GOL 507 A 1 
HETATM 5 C C3 GOL . . . J 7 -7.398 -36.106 -30.423 1 65.32 ? C3 GOL 507 A 1 
HETATM 6 O O3 GOL . . . J 7 -6.325 -36.983 -30.712 1 55.27 ? O3 GOL 507 A 1 
HETATM 7 H H11 GOL . . . J 7 -6.941 -36.865 -28.303 1 81.29 ? H11 GOL 507 A 1 
HETATM 8 H H12 GOL . . . J 7 -8.328 -36.808 -27.617 1 81.29 ? H12 GOL 507 A 1 
HETATM 9 H HO1 GOL . . . J 7 -7.358 -38.947 -28.862 1 72.9 ? HO1 GOL 507 A 1 
HETATM 10 H H2 GOL . . . J 7 -8.748 -37.704 -30.146 1 86.72 ? H2 GOL 507 A 1 
HETATM 11 H HO2 GOL . . . J 7 -9.42 -35.345 -29.252 1 80.03 ? HO2 GOL 507 A 1 
HETATM 12 H H31 GOL . . . J 7 -7.135 -35.353 -29.872 1 78.39 ? H31 GOL 507 A 1 
HETATM 13 H H32 GOL . . . J 7 -7.794 -35.716 -31.217 1 78.39 ? H32 GOL 507 A 1 
HETATM 14 H HO3 GOL . . . J 7 -6.648 -37.768 -30.754 1 66.32 ? HO3 GOL 507 A 1 
#
_model_server_stats.io_time_ms              21 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           487 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           14 
#