data_3CBX
#
_model_server_result.job_id            ayV2ZPyrMwxGhnKrSSifog 
_model_server_result.datetime_utc      '2025-03-26 16:17:20' 
_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          3cbx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":2002}' 
#
_entry.id    3CBX 
#
_exptl.entry_id    3CBX 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              118.174 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (4S)-2-METHYL-2,4-PENTANEDIOL 
_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            3CBX 
_cell.length_a            51.214 
_cell.length_b            61.112 
_cell.length_c            65.818 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3CBX 
_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 
_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
? 2 C N N 
? 2 D N N 
#
_chem_comp.formula           'C6 H14 O2' 
_chem_comp.formula_weight    118.174 
_chem_comp.id                MPD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (4S)-2-METHYL-2,4-PENTANEDIOL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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 C2 MPD sing 237 n n 
C1 H11 MPD sing 238 n n 
C1 H12 MPD sing 239 n n 
C1 H13 MPD sing 240 n n 
C2 O2 MPD sing 241 n n 
C2 CM MPD sing 242 n n 
C2 C3 MPD sing 243 n n 
O2 HO2 MPD sing 244 n n 
CM HM1 MPD sing 245 n n 
CM HM2 MPD sing 246 n n 
CM HM3 MPD sing 247 n n 
C3 C4 MPD sing 248 n n 
C3 H31 MPD sing 249 n n 
C3 H32 MPD sing 250 n n 
C4 O4 MPD sing 251 n n 
C4 C5 MPD sing 252 n n 
C4 H4 MPD sing 253 n n 
O4 HO4 MPD sing 254 n n 
C5 H51 MPD sing 255 n n 
C5 H52 MPD sing 256 n n 
C5 H53 MPD sing 257 n n 
#
_atom_sites.entry_id                     3CBX 
_atom_sites.fract_transf_matrix[1][1]    0.019526 
_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]    0.016363 
_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]    0.015193 
_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 MPD A 1 2001 2001 MPD MPD . 
D 2 MPD A 1 2002 2002 MPD MPD . 
E 3 CL A 1 2004 2004 CL CL . 
F 4 HOH A 1 1002 1002 HOH HOH . 
F 4 HOH A 2 1003 1003 HOH HOH . 
F 4 HOH A 3 1005 1005 HOH HOH . 
F 4 HOH A 4 1006 1006 HOH HOH . 
F 4 HOH A 5 1007 1007 HOH HOH . 
F 4 HOH A 6 1008 1008 HOH HOH . 
F 4 HOH A 7 1009 1009 HOH HOH . 
F 4 HOH A 8 1011 1011 HOH HOH . 
F 4 HOH A 9 1012 1012 HOH HOH . 
F 4 HOH A 10 1013 1013 HOH HOH . 
F 4 HOH A 11 1015 1015 HOH HOH . 
F 4 HOH A 12 1016 1016 HOH HOH . 
F 4 HOH A 13 1017 1017 HOH HOH . 
F 4 HOH A 14 1018 1018 HOH HOH . 
F 4 HOH A 15 1019 1019 HOH HOH . 
F 4 HOH A 16 1020 1020 HOH HOH . 
F 4 HOH A 17 1023 1023 HOH HOH . 
F 4 HOH A 18 1024 1024 HOH HOH . 
F 4 HOH A 19 1025 1025 HOH HOH . 
F 4 HOH A 20 1026 1026 HOH HOH . 
F 4 HOH A 21 1027 1027 HOH HOH . 
F 4 HOH A 22 1028 1028 HOH HOH . 
F 4 HOH A 23 1029 1029 HOH HOH . 
F 4 HOH A 24 1030 1030 HOH HOH . 
F 4 HOH A 25 1031 1031 HOH HOH . 
F 4 HOH A 26 1034 1034 HOH HOH . 
F 4 HOH A 27 1037 1037 HOH HOH . 
F 4 HOH A 28 1038 1038 HOH HOH . 
F 4 HOH A 29 1040 1040 HOH HOH . 
F 4 HOH A 30 1041 1041 HOH HOH . 
F 4 HOH A 31 1043 1043 HOH HOH . 
F 4 HOH A 32 1044 1044 HOH HOH . 
F 4 HOH A 33 1045 1045 HOH HOH . 
F 4 HOH A 34 1052 1052 HOH HOH . 
F 4 HOH A 35 1054 1054 HOH HOH . 
F 4 HOH A 36 1055 1055 HOH HOH . 
F 4 HOH A 37 1058 1058 HOH HOH . 
F 4 HOH A 38 1061 1061 HOH HOH . 
F 4 HOH A 39 1063 1063 HOH HOH . 
F 4 HOH A 40 1064 1064 HOH HOH . 
F 4 HOH A 41 1066 1066 HOH HOH . 
F 4 HOH A 42 1073 1073 HOH HOH . 
F 4 HOH A 43 1074 1074 HOH HOH . 
F 4 HOH A 44 1077 1077 HOH HOH . 
F 4 HOH A 45 1078 1078 HOH HOH . 
F 4 HOH A 46 1079 1079 HOH HOH . 
F 4 HOH A 47 1080 1080 HOH HOH . 
F 4 HOH A 48 1081 1081 HOH HOH . 
F 4 HOH A 49 1082 1082 HOH HOH . 
F 4 HOH A 50 1083 1083 HOH HOH . 
F 4 HOH A 51 1084 1084 HOH HOH . 
F 4 HOH A 52 1085 1085 HOH HOH . 
F 4 HOH A 53 1090 1090 HOH HOH . 
F 4 HOH A 54 1094 1094 HOH HOH . 
F 4 HOH A 55 1096 1096 HOH HOH . 
F 4 HOH A 56 1097 1097 HOH HOH . 
F 4 HOH A 57 1098 1098 HOH HOH . 
F 4 HOH A 58 1099 1099 HOH HOH . 
F 4 HOH A 59 1101 1101 HOH HOH . 
F 4 HOH A 60 1102 1102 HOH HOH . 
F 4 HOH A 61 1103 1103 HOH HOH . 
F 4 HOH A 62 1104 1104 HOH HOH . 
F 4 HOH A 63 1105 1105 HOH HOH . 
F 4 HOH A 64 1106 1106 HOH HOH . 
F 4 HOH A 65 1107 1107 HOH HOH . 
F 4 HOH A 66 1108 1108 HOH HOH . 
F 4 HOH A 67 1112 1112 HOH HOH . 
F 4 HOH A 68 1113 1113 HOH HOH . 
F 4 HOH A 69 1114 1114 HOH HOH . 
F 4 HOH A 70 1115 1115 HOH HOH . 
F 4 HOH A 71 1117 1117 HOH HOH . 
F 4 HOH A 72 1118 1118 HOH HOH . 
F 4 HOH A 73 1119 1119 HOH HOH . 
F 4 HOH A 74 1120 1120 HOH HOH . 
F 4 HOH A 75 1121 1121 HOH HOH . 
G 4 HOH B 1 1001 1001 HOH HOH . 
G 4 HOH B 2 1004 1004 HOH HOH . 
G 4 HOH B 3 1010 1010 HOH HOH . 
G 4 HOH B 4 1014 1014 HOH HOH . 
G 4 HOH B 5 1021 1021 HOH HOH . 
G 4 HOH B 6 1022 1022 HOH HOH . 
G 4 HOH B 7 1032 1032 HOH HOH . 
G 4 HOH B 8 1033 1033 HOH HOH . 
G 4 HOH B 9 1035 1035 HOH HOH . 
G 4 HOH B 10 1036 1036 HOH HOH . 
G 4 HOH B 11 1039 1039 HOH HOH . 
G 4 HOH B 12 1042 1042 HOH HOH . 
G 4 HOH B 13 1046 1046 HOH HOH . 
G 4 HOH B 14 1047 1047 HOH HOH . 
G 4 HOH B 15 1048 1048 HOH HOH . 
G 4 HOH B 16 1049 1049 HOH HOH . 
G 4 HOH B 17 1050 1050 HOH HOH . 
G 4 HOH B 18 1051 1051 HOH HOH . 
G 4 HOH B 19 1053 1053 HOH HOH . 
G 4 HOH B 20 1056 1056 HOH HOH . 
G 4 HOH B 21 1057 1057 HOH HOH . 
G 4 HOH B 22 1059 1059 HOH HOH . 
G 4 HOH B 23 1060 1060 HOH HOH . 
G 4 HOH B 24 1062 1062 HOH HOH . 
G 4 HOH B 25 1065 1065 HOH HOH . 
G 4 HOH B 26 1067 1067 HOH HOH . 
G 4 HOH B 27 1068 1068 HOH HOH . 
G 4 HOH B 28 1069 1069 HOH HOH . 
G 4 HOH B 29 1070 1070 HOH HOH . 
G 4 HOH B 30 1071 1071 HOH HOH . 
G 4 HOH B 31 1072 1072 HOH HOH . 
G 4 HOH B 32 1075 1075 HOH HOH . 
G 4 HOH B 33 1076 1076 HOH HOH . 
G 4 HOH B 34 1086 1086 HOH HOH . 
G 4 HOH B 35 1087 1087 HOH HOH . 
G 4 HOH B 36 1088 1088 HOH HOH . 
G 4 HOH B 37 1089 1089 HOH HOH . 
G 4 HOH B 38 1091 1091 HOH HOH . 
G 4 HOH B 39 1092 1092 HOH HOH . 
G 4 HOH B 40 1093 1093 HOH HOH . 
G 4 HOH B 41 1095 1095 HOH HOH . 
G 4 HOH B 42 1100 1100 HOH HOH . 
G 4 HOH B 43 1109 1109 HOH HOH . 
G 4 HOH B 44 1110 1110 HOH HOH . 
G 4 HOH B 45 1111 1111 HOH HOH . 
G 4 HOH B 46 1116 1116 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 MPD . . . D 2 5.705 15.451 9.346 1 59.5 ? C1 MPD 2002 A 1 
HETATM 2 C C2 MPD . . . D 2 6.838 15.948 8.443 1 57.73 ? C2 MPD 2002 A 1 
HETATM 3 O O2 MPD . . . D 2 6.554 17.313 8.052 1 56.5 ? O2 MPD 2002 A 1 
HETATM 4 C CM MPD . . . D 2 8.15 15.894 9.222 1 56.81 ? CM MPD 2002 A 1 
HETATM 5 C C3 MPD . . . D 2 7.014 15.14 7.159 1 53.95 ? C3 MPD 2002 A 1 
HETATM 6 C C4 MPD . . . D 2 5.728 14.638 6.513 1 48.24 ? C4 MPD 2002 A 1 
HETATM 7 O O4 MPD . . . D 2 5.182 15.594 5.6 1 39.84 ? O4 MPD 2002 A 1 
HETATM 8 C C5 MPD . . . D 2 6.063 13.324 5.822 1 36.43 ? C5 MPD 2002 A 1 
#
_model_server_stats.io_time_ms              5 
_model_server_stats.parse_time_ms           5 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           222 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           8 
#