data_5TDM
#
_model_server_result.job_id            bb_ycWLJljk3JuIaBRWaMQ 
_model_server_result.datetime_utc      '2024-11-05 22:58:49' 
_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          5tdm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":902}' 
#
_entry.id    5TDM 
#
_exptl.entry_id    5TDM 
_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    2 
_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            5TDM 
_cell.length_a            55.379 
_cell.length_b            84.814 
_cell.length_c            193.869 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5TDM 
_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        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 
_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 G N N 
? 7 I 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 O ASN 203 A ASN 203 1_555 E MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? 
metalc ? metalc2 A OD2 ASP 216 A ASP 216 1_555 E MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? 
covale ? covale1 B C GLY 273 B GLY 759 1_555 B N NEP 274 B NEP 760 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale2 B C NEP 274 B NEP 760 1_555 B N ALA 275 B ALA 761 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? 
metalc ? metalc3 B O3P NEP 274 B NEP 760 1_555 H MG MG . B MG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
metalc ? metalc4 D O1A ADP . A ADP 902 1_555 E MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? 
metalc ? metalc5 E MG MG . A MG 903 1_555 J O HOH . A HOH 1038 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? 
metalc ? metalc6 E MG MG . A MG 903 1_555 J O HOH . A HOH 1087 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? 
covale ? covale3 F C8 ADN . A ADN 904 1_555 G O1 GOL . A GOL 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.381 ? 
metalc ? metalc7 H MG MG . B MG 901 1_555 J O HOH . A HOH 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? 
metalc ? metalc8 H MG MG . B MG 901 1_555 K O HOH . B HOH 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? 
metalc ? metalc9 H MG MG . B MG 901 1_555 K O HOH . B HOH 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.899 ? 
#
_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 
#
_atom_sites.entry_id                     5TDM 
_atom_sites.fract_transf_matrix[1][1]    0.018057 
_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]    0.011791 
_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]    0.005158 
_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 3 7A2 A 1 901 901 7A2 7A2 . 
D 4 ADP A 1 902 902 ADP ADP . 
E 5 MG A 1 903 903 MG MG . 
F 6 ADN A 1 904 905 ADN ADN . 
G 7 GOL A 1 905 907 GOL GOL . 
H 5 MG B 1 901 904 MG MG . 
I 7 GOL B 1 902 906 GOL GOL . 
J 8 HOH A 1 1001 1002 HOH HOH . 
J 8 HOH A 2 1002 1003 HOH HOH . 
J 8 HOH A 3 1003 1004 HOH HOH . 
J 8 HOH A 4 1004 1005 HOH HOH . 
J 8 HOH A 5 1005 1006 HOH HOH . 
J 8 HOH A 6 1006 1008 HOH HOH . 
J 8 HOH A 7 1007 1009 HOH HOH . 
J 8 HOH A 8 1008 1010 HOH HOH . 
J 8 HOH A 9 1009 1015 HOH HOH . 
J 8 HOH A 10 1010 1017 HOH HOH . 
J 8 HOH A 11 1011 1018 HOH HOH . 
J 8 HOH A 12 1012 1019 HOH HOH . 
J 8 HOH A 13 1013 1023 HOH HOH . 
J 8 HOH A 14 1014 1024 HOH HOH . 
J 8 HOH A 15 1015 1025 HOH HOH . 
J 8 HOH A 16 1016 1026 HOH HOH . 
J 8 HOH A 17 1017 1029 HOH HOH . 
J 8 HOH A 18 1018 1030 HOH HOH . 
J 8 HOH A 19 1019 1033 HOH HOH . 
J 8 HOH A 20 1020 1038 HOH HOH . 
J 8 HOH A 21 1021 1039 HOH HOH . 
J 8 HOH A 22 1022 1040 HOH HOH . 
J 8 HOH A 23 1023 1047 HOH HOH . 
J 8 HOH A 24 1024 1048 HOH HOH . 
J 8 HOH A 25 1025 1051 HOH HOH . 
J 8 HOH A 26 1026 1056 HOH HOH . 
J 8 HOH A 27 1027 1058 HOH HOH . 
J 8 HOH A 28 1028 1061 HOH HOH . 
J 8 HOH A 29 1029 1062 HOH HOH . 
J 8 HOH A 30 1030 1063 HOH HOH . 
J 8 HOH A 31 1031 1064 HOH HOH . 
J 8 HOH A 32 1032 1065 HOH HOH . 
J 8 HOH A 33 1033 1066 HOH HOH . 
J 8 HOH A 34 1034 1067 HOH HOH . 
J 8 HOH A 35 1035 1068 HOH HOH . 
J 8 HOH A 36 1036 1069 HOH HOH . 
J 8 HOH A 37 1037 1070 HOH HOH . 
J 8 HOH A 38 1038 1071 HOH HOH . 
J 8 HOH A 39 1039 1072 HOH HOH . 
J 8 HOH A 40 1040 1073 HOH HOH . 
J 8 HOH A 41 1041 1074 HOH HOH . 
J 8 HOH A 42 1042 1075 HOH HOH . 
J 8 HOH A 43 1043 1076 HOH HOH . 
J 8 HOH A 44 1044 1077 HOH HOH . 
J 8 HOH A 45 1045 1078 HOH HOH . 
J 8 HOH A 46 1046 1079 HOH HOH . 
J 8 HOH A 47 1047 1081 HOH HOH . 
J 8 HOH A 48 1048 1083 HOH HOH . 
J 8 HOH A 49 1049 1088 HOH HOH . 
J 8 HOH A 50 1050 1089 HOH HOH . 
J 8 HOH A 51 1051 1091 HOH HOH . 
J 8 HOH A 52 1052 1093 HOH HOH . 
J 8 HOH A 53 1053 1094 HOH HOH . 
J 8 HOH A 54 1054 1096 HOH HOH . 
J 8 HOH A 55 1055 1097 HOH HOH . 
J 8 HOH A 56 1056 1099 HOH HOH . 
J 8 HOH A 57 1057 1101 HOH HOH . 
J 8 HOH A 58 1058 1102 HOH HOH . 
J 8 HOH A 59 1059 1103 HOH HOH . 
J 8 HOH A 60 1060 1104 HOH HOH . 
J 8 HOH A 61 1061 1105 HOH HOH . 
J 8 HOH A 62 1062 1106 HOH HOH . 
J 8 HOH A 63 1063 1107 HOH HOH . 
J 8 HOH A 64 1064 1109 HOH HOH . 
J 8 HOH A 65 1065 1110 HOH HOH . 
J 8 HOH A 66 1066 1113 HOH HOH . 
J 8 HOH A 67 1067 1117 HOH HOH . 
J 8 HOH A 68 1068 1118 HOH HOH . 
J 8 HOH A 69 1069 1119 HOH HOH . 
J 8 HOH A 70 1070 1120 HOH HOH . 
J 8 HOH A 71 1071 1122 HOH HOH . 
J 8 HOH A 72 1072 1123 HOH HOH . 
J 8 HOH A 73 1073 1124 HOH HOH . 
J 8 HOH A 74 1074 1125 HOH HOH . 
J 8 HOH A 75 1075 1126 HOH HOH . 
J 8 HOH A 76 1076 1128 HOH HOH . 
J 8 HOH A 77 1077 1130 HOH HOH . 
J 8 HOH A 78 1078 1131 HOH HOH . 
J 8 HOH A 79 1079 1132 HOH HOH . 
J 8 HOH A 80 1080 1135 HOH HOH . 
J 8 HOH A 81 1081 1136 HOH HOH . 
J 8 HOH A 82 1082 1138 HOH HOH . 
J 8 HOH A 83 1083 1139 HOH HOH . 
J 8 HOH A 84 1084 1140 HOH HOH . 
J 8 HOH A 85 1085 1141 HOH HOH . 
J 8 HOH A 86 1086 1143 HOH HOH . 
J 8 HOH A 87 1087 1144 HOH HOH . 
J 8 HOH A 88 1088 1146 HOH HOH . 
J 8 HOH A 89 1089 1149 HOH HOH . 
J 8 HOH A 90 1090 1150 HOH HOH . 
J 8 HOH A 91 1091 1152 HOH HOH . 
J 8 HOH A 92 1092 1154 HOH HOH . 
J 8 HOH A 93 1093 1155 HOH HOH . 
J 8 HOH A 94 1094 1156 HOH HOH . 
J 8 HOH A 95 1095 1157 HOH HOH . 
J 8 HOH A 96 1096 1159 HOH HOH . 
J 8 HOH A 97 1097 1160 HOH HOH . 
J 8 HOH A 98 1098 1161 HOH HOH . 
J 8 HOH A 99 1099 1162 HOH HOH . 
J 8 HOH A 100 1100 1165 HOH HOH . 
J 8 HOH A 101 1101 1166 HOH HOH . 
J 8 HOH A 102 1102 1167 HOH HOH . 
J 8 HOH A 103 1103 1170 HOH HOH . 
J 8 HOH A 104 1104 1171 HOH HOH . 
J 8 HOH A 105 1105 1172 HOH HOH . 
J 8 HOH A 106 1106 1173 HOH HOH . 
J 8 HOH A 107 1107 1175 HOH HOH . 
J 8 HOH A 108 1108 1177 HOH HOH . 
J 8 HOH A 109 1109 1178 HOH HOH . 
J 8 HOH A 110 1110 1179 HOH HOH . 
J 8 HOH A 111 1111 1184 HOH HOH . 
J 8 HOH A 112 1112 1185 HOH HOH . 
J 8 HOH A 113 1113 1187 HOH HOH . 
K 8 HOH B 1 1001 1001 HOH HOH . 
K 8 HOH B 2 1002 1007 HOH HOH . 
K 8 HOH B 3 1003 1011 HOH HOH . 
K 8 HOH B 4 1004 1012 HOH HOH . 
K 8 HOH B 5 1005 1013 HOH HOH . 
K 8 HOH B 6 1006 1014 HOH HOH . 
K 8 HOH B 7 1007 1016 HOH HOH . 
K 8 HOH B 8 1008 1020 HOH HOH . 
K 8 HOH B 9 1009 1021 HOH HOH . 
K 8 HOH B 10 1010 1022 HOH HOH . 
K 8 HOH B 11 1011 1027 HOH HOH . 
K 8 HOH B 12 1012 1028 HOH HOH . 
K 8 HOH B 13 1013 1031 HOH HOH . 
K 8 HOH B 14 1014 1032 HOH HOH . 
K 8 HOH B 15 1015 1034 HOH HOH . 
K 8 HOH B 16 1016 1035 HOH HOH . 
K 8 HOH B 17 1017 1036 HOH HOH . 
K 8 HOH B 18 1018 1037 HOH HOH . 
K 8 HOH B 19 1019 1041 HOH HOH . 
K 8 HOH B 20 1020 1042 HOH HOH . 
K 8 HOH B 21 1021 1043 HOH HOH . 
K 8 HOH B 22 1022 1044 HOH HOH . 
K 8 HOH B 23 1023 1045 HOH HOH . 
K 8 HOH B 24 1024 1046 HOH HOH . 
K 8 HOH B 25 1025 1049 HOH HOH . 
K 8 HOH B 26 1026 1050 HOH HOH . 
K 8 HOH B 27 1027 1052 HOH HOH . 
K 8 HOH B 28 1028 1053 HOH HOH . 
K 8 HOH B 29 1029 1054 HOH HOH . 
K 8 HOH B 30 1030 1055 HOH HOH . 
K 8 HOH B 31 1031 1057 HOH HOH . 
K 8 HOH B 32 1032 1059 HOH HOH . 
K 8 HOH B 33 1033 1060 HOH HOH . 
K 8 HOH B 34 1034 1080 HOH HOH . 
K 8 HOH B 35 1035 1082 HOH HOH . 
K 8 HOH B 36 1036 1084 HOH HOH . 
K 8 HOH B 37 1037 1085 HOH HOH . 
K 8 HOH B 38 1038 1086 HOH HOH . 
K 8 HOH B 39 1039 1087 HOH HOH . 
K 8 HOH B 40 1040 1090 HOH HOH . 
K 8 HOH B 41 1041 1092 HOH HOH . 
K 8 HOH B 42 1042 1095 HOH HOH . 
K 8 HOH B 43 1043 1098 HOH HOH . 
K 8 HOH B 44 1044 1100 HOH HOH . 
K 8 HOH B 45 1045 1108 HOH HOH . 
K 8 HOH B 46 1046 1111 HOH HOH . 
K 8 HOH B 47 1047 1112 HOH HOH . 
K 8 HOH B 48 1048 1114 HOH HOH . 
K 8 HOH B 49 1049 1115 HOH HOH . 
K 8 HOH B 50 1050 1116 HOH HOH . 
K 8 HOH B 51 1051 1121 HOH HOH . 
K 8 HOH B 52 1052 1127 HOH HOH . 
K 8 HOH B 53 1053 1129 HOH HOH . 
K 8 HOH B 54 1054 1133 HOH HOH . 
K 8 HOH B 55 1055 1134 HOH HOH . 
K 8 HOH B 56 1056 1137 HOH HOH . 
K 8 HOH B 57 1057 1142 HOH HOH . 
K 8 HOH B 58 1058 1145 HOH HOH . 
K 8 HOH B 59 1059 1147 HOH HOH . 
K 8 HOH B 60 1060 1148 HOH HOH . 
K 8 HOH B 61 1061 1151 HOH HOH . 
K 8 HOH B 62 1062 1153 HOH HOH . 
K 8 HOH B 63 1063 1158 HOH HOH . 
K 8 HOH B 64 1064 1163 HOH HOH . 
K 8 HOH B 65 1065 1164 HOH HOH . 
K 8 HOH B 66 1066 1168 HOH HOH . 
K 8 HOH B 67 1067 1169 HOH HOH . 
K 8 HOH B 68 1068 1174 HOH HOH . 
K 8 HOH B 69 1069 1176 HOH HOH . 
K 8 HOH B 70 1070 1180 HOH HOH . 
K 8 HOH B 71 1071 1181 HOH HOH . 
K 8 HOH B 72 1072 1182 HOH HOH . 
K 8 HOH B 73 1073 1183 HOH HOH . 
K 8 HOH B 74 1074 1186 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 . . . I 7 2.59 5.858 55.307 1 85.22 ? C1 GOL 902 B 1 
HETATM 2 O O1 GOL . . . I 7 1.69 6.189 56.355 1 71.58 ? O1 GOL 902 B 1 
HETATM 3 C C2 GOL . . . I 7 3.727 6.871 55.235 1 91.04 ? C2 GOL 902 B 1 
HETATM 4 O O2 GOL . . . I 7 4.281 7.043 56.515 1 58.18 ? O2 GOL 902 B 1 
HETATM 5 C C3 GOL . . . I 7 4.802 6.363 54.273 1 107.42 ? C3 GOL 902 B 1 
HETATM 6 O O3 GOL . . . I 7 5.905 7.242 54.289 1 111.61 ? O3 GOL 902 B 1 
HETATM 7 H H11 GOL . . . I 7 2.055 5.842 54.358 1 102.27 ? H11 GOL 902 B 1 
HETATM 8 H H12 GOL . . . I 7 3 4.863 55.479 1 102.27 ? H12 GOL 902 B 1 
HETATM 9 H HO1 GOL . . . I 7 0.933 5.566 56.345 1 85.9 ? HO1 GOL 902 B 1 
HETATM 10 H H2 GOL . . . I 7 3.336 7.819 54.864 1 109.24 ? H2 GOL 902 B 1 
HETATM 11 H HO2 GOL . . . I 7 4.638 6.188 56.834 1 69.82 ? HO2 GOL 902 B 1 
HETATM 12 H H31 GOL . . . I 7 4.395 6.301 53.264 1 128.9 ? H31 GOL 902 B 1 
HETATM 13 H H32 GOL . . . I 7 5.122 5.365 54.573 1 128.9 ? H32 GOL 902 B 1 
HETATM 14 H HO3 GOL . . . I 7 5.594 8.159 54.139 1 133.93 ? HO3 GOL 902 B 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    56 
_model_server_stats.query_time_ms           288 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           14 
#