data_3VF7
#
_model_server_result.job_id            O1pz7xdoasgWksCuVzqhnQ 
_model_server_result.datetime_utc      '2024-11-15 07:55:01' 
_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          3vf7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":208}' 
#
_entry.id    3VF7 
#
_exptl.entry_id    3VF7 
_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    5 
_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            3VF7 
_cell.length_a            57.82 
_cell.length_b            86.242 
_cell.length_c            46.005 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VF7 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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,N,O 
_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 G N N 
? 5 H N N 
? 5 I N N 
? 5 J N N 
? 5 M 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 D NA NA . A NA 202 1_555 N O HOH . A HOH 1016 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.688 ? 
metalc ? metalc2 D NA NA . A NA 202 1_555 N O HOH . A HOH 1041 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
metalc ? metalc3 D NA NA . A NA 202 1_555 N O HOH . A HOH 1063 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? 
metalc ? metalc4 D NA NA . A NA 202 1_555 N O HOH . A HOH 1071 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? 
metalc ? metalc5 D NA NA . A NA 202 1_555 N O HOH . A HOH 1076 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
metalc ? metalc6 D NA NA . A NA 202 1_555 N O HOH . A HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? 
metalc ? metalc7 B O ASP 60 B ASP 60 1_555 K NA NA . B NA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? 
metalc ? metalc8 K NA NA . B NA 501 1_555 O O HOH . B HOH 630 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? 
metalc ? metalc9 K NA NA . B NA 501 1_555 O O HOH . B HOH 631 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? 
metalc ? metalc10 K NA NA . B NA 501 1_555 O O HOH . B HOH 632 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? 
metalc ? metalc11 K NA NA . B NA 501 1_555 O O HOH . B HOH 634 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? 
metalc ? metalc12 K NA NA . B NA 501 1_555 O O HOH . B HOH 674 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? 
#
_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 214 n n 
C1 C2 GOL sing 215 n n 
C1 H11 GOL sing 216 n n 
C1 H12 GOL sing 217 n n 
O1 HO1 GOL sing 218 n n 
C2 O2 GOL sing 219 n n 
C2 C3 GOL sing 220 n n 
C2 H2 GOL sing 221 n n 
O2 HO2 GOL sing 222 n n 
C3 O3 GOL sing 223 n n 
C3 H31 GOL sing 224 n n 
C3 H32 GOL sing 225 n n 
O3 HO3 GOL sing 226 n n 
#
_atom_sites.entry_id                     3VF7 
_atom_sites.fract_transf_matrix[1][1]    0.017295 
_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]    0.011595 
_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]    0.021737 
_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
C 2 031 A 1 201 201 031 031 . 
D 3 NA A 1 202 502 NA NA . 
E 4 CL A 1 203 512 CL CL . 
F 4 CL A 1 204 513 CL CL . 
G 5 GOL A 1 205 521 GOL GOL . 
H 5 GOL A 1 206 523 GOL GOL . 
I 5 GOL A 1 207 524 GOL GOL . 
J 5 GOL A 1 208 525 GOL GOL . 
K 3 NA B 1 501 501 NA NA . 
L 4 CL B 1 502 511 CL CL . 
M 5 GOL B 1 503 522 GOL GOL . 
N 6 HOH A 1 1001 1001 HOH HOH . 
N 6 HOH A 2 1002 1002 HOH HOH . 
N 6 HOH A 3 1003 1004 HOH HOH . 
N 6 HOH A 4 1004 1005 HOH HOH . 
N 6 HOH A 5 1005 1007 HOH HOH . 
N 6 HOH A 6 1006 1008 HOH HOH . 
N 6 HOH A 7 1007 1009 HOH HOH . 
N 6 HOH A 8 1008 1016 HOH HOH . 
N 6 HOH A 9 1009 1017 HOH HOH . 
N 6 HOH A 10 1010 1019 HOH HOH . 
N 6 HOH A 11 1011 1021 HOH HOH . 
N 6 HOH A 12 1012 1022 HOH HOH . 
N 6 HOH A 13 1013 1023 HOH HOH . 
N 6 HOH A 14 1014 1025 HOH HOH . 
N 6 HOH A 15 1015 1026 HOH HOH . 
N 6 HOH A 16 1016 1027 HOH HOH . 
N 6 HOH A 17 1017 1028 HOH HOH . 
N 6 HOH A 18 1018 1031 HOH HOH . 
N 6 HOH A 19 1019 1032 HOH HOH . 
N 6 HOH A 20 1020 1033 HOH HOH . 
N 6 HOH A 21 1021 1035 HOH HOH . 
N 6 HOH A 22 1022 1036 HOH HOH . 
N 6 HOH A 23 1023 1037 HOH HOH . 
N 6 HOH A 24 1024 1038 HOH HOH . 
N 6 HOH A 25 1025 1039 HOH HOH . 
N 6 HOH A 26 1026 1040 HOH HOH . 
N 6 HOH A 27 1027 1044 HOH HOH . 
N 6 HOH A 28 1028 1045 HOH HOH . 
N 6 HOH A 29 1029 1046 HOH HOH . 
N 6 HOH A 30 1030 1047 HOH HOH . 
N 6 HOH A 31 1031 1049 HOH HOH . 
N 6 HOH A 32 1032 1050 HOH HOH . 
N 6 HOH A 33 1033 1052 HOH HOH . 
N 6 HOH A 34 1034 1053 HOH HOH . 
N 6 HOH A 35 1035 1054 HOH HOH . 
N 6 HOH A 36 1036 1056 HOH HOH . 
N 6 HOH A 37 1037 1058 HOH HOH . 
N 6 HOH A 38 1038 1060 HOH HOH . 
N 6 HOH A 39 1039 1061 HOH HOH . 
N 6 HOH A 40 1040 1063 HOH HOH . 
N 6 HOH A 41 1041 1064 HOH HOH . 
N 6 HOH A 42 1042 1066 HOH HOH . 
N 6 HOH A 43 1043 1067 HOH HOH . 
N 6 HOH A 44 1044 1069 HOH HOH . 
N 6 HOH A 45 1045 1071 HOH HOH . 
N 6 HOH A 46 1046 1072 HOH HOH . 
N 6 HOH A 47 1047 1074 HOH HOH . 
N 6 HOH A 48 1048 1075 HOH HOH . 
N 6 HOH A 49 1049 1076 HOH HOH . 
N 6 HOH A 50 1050 1077 HOH HOH . 
N 6 HOH A 51 1051 1078 HOH HOH . 
N 6 HOH A 52 1052 1080 HOH HOH . 
N 6 HOH A 53 1053 1081 HOH HOH . 
N 6 HOH A 54 1054 1083 HOH HOH . 
N 6 HOH A 55 1055 1084 HOH HOH . 
N 6 HOH A 56 1056 1087 HOH HOH . 
N 6 HOH A 57 1057 1089 HOH HOH . 
N 6 HOH A 58 1058 1090 HOH HOH . 
N 6 HOH A 59 1059 1094 HOH HOH . 
N 6 HOH A 60 1060 1095 HOH HOH . 
N 6 HOH A 61 1061 1098 HOH HOH . 
N 6 HOH A 62 1062 1099 HOH HOH . 
N 6 HOH A 63 1063 1100 HOH HOH . 
N 6 HOH A 64 1064 1101 HOH HOH . 
N 6 HOH A 65 1065 1102 HOH HOH . 
N 6 HOH A 66 1066 1103 HOH HOH . 
N 6 HOH A 67 1067 1104 HOH HOH . 
N 6 HOH A 68 1068 1114 HOH HOH . 
N 6 HOH A 69 1069 1115 HOH HOH . 
N 6 HOH A 70 1070 1117 HOH HOH . 
N 6 HOH A 71 1071 1119 HOH HOH . 
N 6 HOH A 72 1072 1121 HOH HOH . 
N 6 HOH A 73 1073 1123 HOH HOH . 
N 6 HOH A 74 1074 1124 HOH HOH . 
N 6 HOH A 75 1075 1125 HOH HOH . 
N 6 HOH A 76 1076 1127 HOH HOH . 
N 6 HOH A 77 1077 1131 HOH HOH . 
N 6 HOH A 78 1078 1132 HOH HOH . 
N 6 HOH A 79 1079 1133 HOH HOH . 
N 6 HOH A 80 1080 1135 HOH HOH . 
N 6 HOH A 81 1081 1137 HOH HOH . 
N 6 HOH A 82 1082 1138 HOH HOH . 
N 6 HOH A 83 1083 1140 HOH HOH . 
N 6 HOH A 84 1084 1144 HOH HOH . 
N 6 HOH A 85 1085 1148 HOH HOH . 
N 6 HOH A 86 1086 1154 HOH HOH . 
N 6 HOH A 87 1087 1157 HOH HOH . 
N 6 HOH A 88 1088 1158 HOH HOH . 
N 6 HOH A 89 1089 1165 HOH HOH . 
N 6 HOH A 90 1090 1167 HOH HOH . 
N 6 HOH A 91 1091 1172 HOH HOH . 
N 6 HOH A 92 1092 1174 HOH HOH . 
N 6 HOH A 93 1093 1183 HOH HOH . 
N 6 HOH A 94 1094 1184 HOH HOH . 
N 6 HOH A 95 1095 1185 HOH HOH . 
N 6 HOH A 96 1096 1186 HOH HOH . 
N 6 HOH A 97 1097 1187 HOH HOH . 
N 6 HOH A 98 1098 1188 HOH HOH . 
N 6 HOH A 99 1099 1189 HOH HOH . 
N 6 HOH A 100 1100 1197 HOH HOH . 
N 6 HOH A 101 1101 1198 HOH HOH . 
N 6 HOH A 102 1102 1199 HOH HOH . 
N 6 HOH A 103 1103 1204 HOH HOH . 
N 6 HOH A 104 1104 1207 HOH HOH . 
N 6 HOH A 105 1105 1208 HOH HOH . 
N 6 HOH A 106 1106 1209 HOH HOH . 
N 6 HOH A 107 1107 1211 HOH HOH . 
O 6 HOH B 1 601 1003 HOH HOH . 
O 6 HOH B 2 602 1006 HOH HOH . 
O 6 HOH B 3 603 1010 HOH HOH . 
O 6 HOH B 4 604 1011 HOH HOH . 
O 6 HOH B 5 605 1012 HOH HOH . 
O 6 HOH B 6 606 1013 HOH HOH . 
O 6 HOH B 7 607 1014 HOH HOH . 
O 6 HOH B 8 608 1015 HOH HOH . 
O 6 HOH B 9 609 1018 HOH HOH . 
O 6 HOH B 10 610 1020 HOH HOH . 
O 6 HOH B 11 611 1024 HOH HOH . 
O 6 HOH B 12 612 1029 HOH HOH . 
O 6 HOH B 13 613 1030 HOH HOH . 
O 6 HOH B 14 614 1034 HOH HOH . 
O 6 HOH B 15 615 1041 HOH HOH . 
O 6 HOH B 16 616 1042 HOH HOH . 
O 6 HOH B 17 617 1043 HOH HOH . 
O 6 HOH B 18 618 1048 HOH HOH . 
O 6 HOH B 19 619 1051 HOH HOH . 
O 6 HOH B 20 620 1055 HOH HOH . 
O 6 HOH B 21 621 1057 HOH HOH . 
O 6 HOH B 22 622 1059 HOH HOH . 
O 6 HOH B 23 623 1062 HOH HOH . 
O 6 HOH B 24 624 1065 HOH HOH . 
O 6 HOH B 25 625 1068 HOH HOH . 
O 6 HOH B 26 626 1070 HOH HOH . 
O 6 HOH B 27 627 1073 HOH HOH . 
O 6 HOH B 28 628 1079 HOH HOH . 
O 6 HOH B 29 629 1082 HOH HOH . 
O 6 HOH B 30 630 1085 HOH HOH . 
O 6 HOH B 31 631 1086 HOH HOH . 
O 6 HOH B 32 632 1088 HOH HOH . 
O 6 HOH B 33 633 1091 HOH HOH . 
O 6 HOH B 34 634 1092 HOH HOH . 
O 6 HOH B 35 635 1093 HOH HOH . 
O 6 HOH B 36 636 1096 HOH HOH . 
O 6 HOH B 37 637 1097 HOH HOH . 
O 6 HOH B 38 638 1105 HOH HOH . 
O 6 HOH B 39 639 1106 HOH HOH . 
O 6 HOH B 40 640 1107 HOH HOH . 
O 6 HOH B 41 641 1108 HOH HOH . 
O 6 HOH B 42 642 1109 HOH HOH . 
O 6 HOH B 43 643 1110 HOH HOH . 
O 6 HOH B 44 644 1111 HOH HOH . 
O 6 HOH B 45 645 1112 HOH HOH . 
O 6 HOH B 46 646 1113 HOH HOH . 
O 6 HOH B 47 647 1116 HOH HOH . 
O 6 HOH B 48 648 1118 HOH HOH . 
O 6 HOH B 49 649 1122 HOH HOH . 
O 6 HOH B 50 650 1126 HOH HOH . 
O 6 HOH B 51 651 1128 HOH HOH . 
O 6 HOH B 52 652 1130 HOH HOH . 
O 6 HOH B 53 653 1134 HOH HOH . 
O 6 HOH B 54 654 1136 HOH HOH . 
O 6 HOH B 55 655 1141 HOH HOH . 
O 6 HOH B 56 656 1142 HOH HOH . 
O 6 HOH B 57 657 1143 HOH HOH . 
O 6 HOH B 58 658 1145 HOH HOH . 
O 6 HOH B 59 659 1146 HOH HOH . 
O 6 HOH B 60 660 1149 HOH HOH . 
O 6 HOH B 61 661 1150 HOH HOH . 
O 6 HOH B 62 662 1151 HOH HOH . 
O 6 HOH B 63 663 1155 HOH HOH . 
O 6 HOH B 64 664 1156 HOH HOH . 
O 6 HOH B 65 665 1160 HOH HOH . 
O 6 HOH B 66 666 1164 HOH HOH . 
O 6 HOH B 67 667 1166 HOH HOH . 
O 6 HOH B 68 668 1171 HOH HOH . 
O 6 HOH B 69 669 1175 HOH HOH . 
O 6 HOH B 70 670 1190 HOH HOH . 
O 6 HOH B 71 671 1191 HOH HOH . 
O 6 HOH B 72 672 1193 HOH HOH . 
O 6 HOH B 73 673 1194 HOH HOH . 
O 6 HOH B 74 674 1195 HOH HOH . 
O 6 HOH B 75 675 1196 HOH HOH . 
O 6 HOH B 76 676 1200 HOH HOH . 
O 6 HOH B 77 677 1201 HOH HOH . 
O 6 HOH B 78 678 1203 HOH HOH . 
O 6 HOH B 79 679 1206 HOH HOH . 
O 6 HOH B 80 680 1210 HOH HOH . 
O 6 HOH B 81 681 1212 HOH HOH . 
O 6 HOH B 82 682 1213 HOH HOH . 
O 6 HOH B 83 683 1215 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 5 13.544 40.321 38.628 0.5 24.59 ? C1 GOL 208 A 1 
HETATM 2 O O1 GOL . . . J 5 12.635 39.529 37.869 0.5 18.75 ? O1 GOL 208 A 1 
HETATM 3 C C2 GOL . . . J 5 13.72 39.705 40.018 0.5 22.75 ? C2 GOL 208 A 1 
HETATM 4 O O2 GOL . . . J 5 12.364 39.425 40.426 0.5 26.94 ? O2 GOL 208 A 1 
HETATM 5 C C3 GOL . . . J 5 14.522 38.422 39.963 0.5 25.28 ? C3 GOL 208 A 1 
HETATM 6 O O3 GOL . . . J 5 15.898 38.5 40.32 0.5 16.17 ? O3 GOL 208 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           257 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           6 
#