data_6PDN
#
_model_server_result.job_id            vYBM3LhUrrYHlUYG6Yv28g 
_model_server_result.datetime_utc      '2024-12-23 06:24:02' 
_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          6pdn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":901}' 
#
_entry.id    6PDN 
#
_exptl.entry_id    6PDN 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_entity.pdbx_number_of_molecules    1 
_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            6PDN 
_cell.length_a            98.001 
_cell.length_b            98.001 
_cell.length_c            80.248 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PDN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 A C SER 261 A SER 260 1_555 A N SEP 262 A SEP 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? 
covale ? covale2 A C SEP 262 A SEP 261 1_555 A N GLU 263 A GLU 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? 
#
_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 129 n n 
C1 C2 GOL sing 130 n n 
C1 H11 GOL sing 131 n n 
C1 H12 GOL sing 132 n n 
O1 HO1 GOL sing 133 n n 
C2 O2 GOL sing 134 n n 
C2 C3 GOL sing 135 n n 
C2 H2 GOL sing 136 n n 
O2 HO2 GOL sing 137 n n 
C3 O3 GOL sing 138 n n 
C3 H31 GOL sing 139 n n 
C3 H32 GOL sing 140 n n 
O3 HO3 GOL sing 141 n n 
#
_atom_sites.entry_id                     6PDN 
_atom_sites.fract_transf_matrix[1][1]    0.010204 
_atom_sites.fract_transf_matrix[1][2]    0.005891 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011783 
_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]    0.012461 
_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 OD4 A 1 900 900 OD4 292 . 
D 4 GOL A 1 901 901 GOL GOL . 
E 5 HOH A 1 1001 1048 HOH HOH . 
E 5 HOH A 2 1002 1133 HOH HOH . 
E 5 HOH A 3 1003 1046 HOH HOH . 
E 5 HOH A 4 1004 1014 HOH HOH . 
E 5 HOH A 5 1005 1051 HOH HOH . 
E 5 HOH A 6 1006 1035 HOH HOH . 
E 5 HOH A 7 1007 1123 HOH HOH . 
E 5 HOH A 8 1008 1065 HOH HOH . 
E 5 HOH A 9 1009 1005 HOH HOH . 
E 5 HOH A 10 1010 1089 HOH HOH . 
E 5 HOH A 11 1011 1026 HOH HOH . 
E 5 HOH A 12 1012 1043 HOH HOH . 
E 5 HOH A 13 1013 1022 HOH HOH . 
E 5 HOH A 14 1014 1038 HOH HOH . 
E 5 HOH A 15 1015 1009 HOH HOH . 
E 5 HOH A 16 1016 1015 HOH HOH . 
E 5 HOH A 17 1017 1025 HOH HOH . 
E 5 HOH A 18 1018 1064 HOH HOH . 
E 5 HOH A 19 1019 1067 HOH HOH . 
E 5 HOH A 20 1020 1088 HOH HOH . 
E 5 HOH A 21 1021 1090 HOH HOH . 
E 5 HOH A 22 1022 1003 HOH HOH . 
E 5 HOH A 23 1023 1019 HOH HOH . 
E 5 HOH A 24 1024 1113 HOH HOH . 
E 5 HOH A 25 1025 1007 HOH HOH . 
E 5 HOH A 26 1026 1066 HOH HOH . 
E 5 HOH A 27 1027 1030 HOH HOH . 
E 5 HOH A 28 1028 1012 HOH HOH . 
E 5 HOH A 29 1029 1140 HOH HOH . 
E 5 HOH A 30 1030 1044 HOH HOH . 
E 5 HOH A 31 1031 1085 HOH HOH . 
E 5 HOH A 32 1032 1057 HOH HOH . 
E 5 HOH A 33 1033 1052 HOH HOH . 
E 5 HOH A 34 1034 1002 HOH HOH . 
E 5 HOH A 35 1035 1001 HOH HOH . 
E 5 HOH A 36 1036 1061 HOH HOH . 
E 5 HOH A 37 1037 1021 HOH HOH . 
E 5 HOH A 38 1038 1004 HOH HOH . 
E 5 HOH A 39 1039 1138 HOH HOH . 
E 5 HOH A 40 1040 1081 HOH HOH . 
E 5 HOH A 41 1041 1100 HOH HOH . 
E 5 HOH A 42 1042 1062 HOH HOH . 
E 5 HOH A 43 1043 1124 HOH HOH . 
E 5 HOH A 44 1044 1118 HOH HOH . 
E 5 HOH A 45 1045 1034 HOH HOH . 
E 5 HOH A 46 1046 1006 HOH HOH . 
E 5 HOH A 47 1047 1122 HOH HOH . 
E 5 HOH A 48 1048 1031 HOH HOH . 
E 5 HOH A 49 1049 1049 HOH HOH . 
E 5 HOH A 50 1050 1008 HOH HOH . 
E 5 HOH A 51 1051 1128 HOH HOH . 
E 5 HOH A 52 1052 1134 HOH HOH . 
E 5 HOH A 53 1053 1077 HOH HOH . 
E 5 HOH A 54 1054 1011 HOH HOH . 
E 5 HOH A 55 1055 1070 HOH HOH . 
E 5 HOH A 56 1056 1029 HOH HOH . 
E 5 HOH A 57 1057 1023 HOH HOH . 
E 5 HOH A 58 1058 1036 HOH HOH . 
E 5 HOH A 59 1059 1053 HOH HOH . 
E 5 HOH A 60 1060 1042 HOH HOH . 
E 5 HOH A 61 1061 1060 HOH HOH . 
E 5 HOH A 62 1062 1056 HOH HOH . 
E 5 HOH A 63 1063 1139 HOH HOH . 
E 5 HOH A 64 1064 1059 HOH HOH . 
E 5 HOH A 65 1065 1039 HOH HOH . 
E 5 HOH A 66 1066 1074 HOH HOH . 
E 5 HOH A 67 1067 1013 HOH HOH . 
E 5 HOH A 68 1068 1107 HOH HOH . 
E 5 HOH A 69 1069 1095 HOH HOH . 
E 5 HOH A 70 1070 1018 HOH HOH . 
E 5 HOH A 71 1071 1082 HOH HOH . 
E 5 HOH A 72 1072 1080 HOH HOH . 
E 5 HOH A 73 1073 1099 HOH HOH . 
E 5 HOH A 74 1074 1073 HOH HOH . 
E 5 HOH A 75 1075 1114 HOH HOH . 
E 5 HOH A 76 1076 1027 HOH HOH . 
E 5 HOH A 77 1077 1040 HOH HOH . 
E 5 HOH A 78 1078 1063 HOH HOH . 
E 5 HOH A 79 1079 1033 HOH HOH . 
E 5 HOH A 80 1080 1101 HOH HOH . 
E 5 HOH A 81 1081 1132 HOH HOH . 
E 5 HOH A 82 1082 1108 HOH HOH . 
E 5 HOH A 83 1083 1137 HOH HOH . 
E 5 HOH A 84 1084 1109 HOH HOH . 
E 5 HOH A 85 1085 1097 HOH HOH . 
E 5 HOH A 86 1086 1072 HOH HOH . 
E 5 HOH A 87 1087 1079 HOH HOH . 
F 5 HOH B 1 101 1141 HOH HOH . 
F 5 HOH B 2 102 1096 HOH HOH . 
F 5 HOH B 3 103 1054 HOH HOH . 
F 5 HOH B 4 104 1078 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 . . . D 4 104.668 101.972 6.748 1 67.12 ? C1 GOL 901 A 1 
HETATM 2 O O1 GOL . . . D 4 106.032 102.222 7.08 1 65.79 ? O1 GOL 901 A 1 
HETATM 3 C C2 GOL . . . D 4 103.715 102.372 7.863 1 69.17 ? C2 GOL 901 A 1 
HETATM 4 O O2 GOL . . . D 4 102.537 102.942 7.303 1 55.33 ? O2 GOL 901 A 1 
HETATM 5 C C3 GOL . . . D 4 103.298 101.233 8.773 1 72.98 ? C3 GOL 901 A 1 
HETATM 6 O O3 GOL . . . D 4 102.1 101.545 9.481 1 70.76 ? O3 GOL 901 A 1 
#
_model_server_stats.io_time_ms              51 
_model_server_stats.parse_time_ms           33 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           233 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           6 
#