data_6PD5
#
_model_server_result.job_id            NZd6LuAsQZAaShKQ7jI4hg 
_model_server_result.datetime_utc      '2024-12-27 01:46:49' 
_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          6pd5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":1113}' 
#
_entry.id    6PD5 
#
_exptl.entry_id    6PD5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          3 
_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            6PD5 
_cell.length_a            108.056 
_cell.length_b            108.056 
_cell.length_c            419.819 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PD5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        155 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3 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,N,O,P,Q,R,S,T 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -54.028 93.579241 0 
3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -108.056 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 M N N 
? 3 N N N 
? 3 O 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
disulf ? disulf1 A SG CYS 19 A CYS 14 1_555 A SG CYS 482 A CYS 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
disulf ? disulf2 A SG CYS 57 A CYS 52 1_555 A SG CYS 289 A CYS 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
disulf ? disulf3 A SG CYS 70 A CYS 65 1_555 A SG CYS 82 A CYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
disulf ? disulf4 A SG CYS 105 A CYS 100 1_555 A SG CYS 150 A CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? 
disulf ? disulf5 A SG CYS 293 A CYS 288 1_555 A SG CYS 317 A CYS 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? 
disulf ? disulf6 A SG CYS 489 A CYS 1011 1_555 A SG CYS 493 A CYS 1015 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? 
covale ? covale1 A ND2 ASN 38 A ASN 33 1_555 P C1 NAG . A NAG 1115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? 
covale ? covale2 A ND2 ASN 169 A ASN 164 1_555 S C1 NAG . A NAG 1118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale3 A ND2 ASN 180 A ASN 175 1_555 Q C1 NAG . A NAG 1116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? 
covale ? covale4 A ND2 ASN 499 A ASN 1021 1_555 R C1 NAG . A NAG 1117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
#
_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                     6PD5 
_atom_sites.fract_transf_matrix[1][1]    0.009254 
_atom_sites.fract_transf_matrix[1][2]    0.005343 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010686 
_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]    0.002382 
_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
B 2 SO4 A 1 1101 1 SO4 SO4 . 
C 2 SO4 A 1 1102 2 SO4 SO4 . 
D 2 SO4 A 1 1103 3 SO4 SO4 . 
E 2 SO4 A 1 1104 4 SO4 SO4 . 
F 2 SO4 A 1 1105 5 SO4 SO4 . 
G 2 SO4 A 1 1106 6 SO4 SO4 . 
H 2 SO4 A 1 1107 7 SO4 SO4 . 
I 2 SO4 A 1 1108 9 SO4 SO4 . 
J 2 SO4 A 1 1109 10 SO4 SO4 . 
K 2 SO4 A 1 1110 11 SO4 SO4 . 
L 2 SO4 A 1 1111 12 SO4 SO4 . 
M 3 GOL A 1 1112 13 GOL GOL . 
N 3 GOL A 1 1113 14 GOL GOL . 
O 3 GOL A 1 1114 15 GOL GOL . 
P 4 NAG A 1 1115 1 NAG NAG . 
Q 4 NAG A 1 1116 2 NAG NAG . 
R 4 NAG A 1 1117 3 NAG NAG . 
S 4 NAG A 1 1118 4 NAG NAG . 
T 5 HOH A 1 1201 19 HOH HOH . 
T 5 HOH A 2 1202 28 HOH HOH . 
T 5 HOH A 3 1203 79 HOH HOH . 
T 5 HOH A 4 1204 70 HOH HOH . 
T 5 HOH A 5 1205 27 HOH HOH . 
T 5 HOH A 6 1206 75 HOH HOH . 
T 5 HOH A 7 1207 26 HOH HOH . 
T 5 HOH A 8 1208 7 HOH HOH . 
T 5 HOH A 9 1209 45 HOH HOH . 
T 5 HOH A 10 1210 20 HOH HOH . 
T 5 HOH A 11 1211 80 HOH HOH . 
T 5 HOH A 12 1212 103 HOH HOH . 
T 5 HOH A 13 1213 5 HOH HOH . 
T 5 HOH A 14 1214 92 HOH HOH . 
T 5 HOH A 15 1215 30 HOH HOH . 
T 5 HOH A 16 1216 51 HOH HOH . 
T 5 HOH A 17 1217 21 HOH HOH . 
T 5 HOH A 18 1218 35 HOH HOH . 
T 5 HOH A 19 1219 87 HOH HOH . 
T 5 HOH A 20 1220 8 HOH HOH . 
T 5 HOH A 21 1221 99 HOH HOH . 
T 5 HOH A 22 1222 85 HOH HOH . 
T 5 HOH A 23 1223 84 HOH HOH . 
T 5 HOH A 24 1224 59 HOH HOH . 
T 5 HOH A 25 1225 63 HOH HOH . 
T 5 HOH A 26 1226 88 HOH HOH . 
T 5 HOH A 27 1227 4 HOH HOH . 
T 5 HOH A 28 1228 2 HOH HOH . 
T 5 HOH A 29 1229 74 HOH HOH . 
T 5 HOH A 30 1230 44 HOH HOH . 
T 5 HOH A 31 1231 10 HOH HOH . 
T 5 HOH A 32 1232 96 HOH HOH . 
T 5 HOH A 33 1233 58 HOH HOH . 
T 5 HOH A 34 1234 90 HOH HOH . 
T 5 HOH A 35 1235 98 HOH HOH . 
T 5 HOH A 36 1236 3 HOH HOH . 
T 5 HOH A 37 1237 32 HOH HOH . 
T 5 HOH A 38 1238 60 HOH HOH . 
T 5 HOH A 39 1239 97 HOH HOH . 
T 5 HOH A 40 1240 39 HOH HOH . 
T 5 HOH A 41 1241 50 HOH HOH . 
T 5 HOH A 42 1242 6 HOH HOH . 
T 5 HOH A 43 1243 66 HOH HOH . 
T 5 HOH A 44 1244 37 HOH HOH . 
T 5 HOH A 45 1245 104 HOH HOH . 
T 5 HOH A 46 1246 42 HOH HOH . 
T 5 HOH A 47 1247 57 HOH HOH . 
T 5 HOH A 48 1248 38 HOH HOH . 
T 5 HOH A 49 1249 76 HOH HOH . 
T 5 HOH A 50 1250 9 HOH HOH . 
T 5 HOH A 51 1251 13 HOH HOH . 
T 5 HOH A 52 1252 89 HOH HOH . 
T 5 HOH A 53 1253 33 HOH HOH . 
T 5 HOH A 54 1254 101 HOH HOH . 
T 5 HOH A 55 1255 56 HOH HOH . 
T 5 HOH A 56 1256 1 HOH HOH . 
T 5 HOH A 57 1257 25 HOH HOH . 
T 5 HOH A 58 1258 14 HOH HOH . 
T 5 HOH A 59 1259 43 HOH HOH . 
T 5 HOH A 60 1260 93 HOH HOH . 
T 5 HOH A 61 1261 16 HOH HOH . 
T 5 HOH A 62 1262 22 HOH HOH . 
T 5 HOH A 63 1263 52 HOH HOH . 
T 5 HOH A 64 1264 69 HOH HOH . 
T 5 HOH A 65 1265 73 HOH HOH . 
T 5 HOH A 66 1266 78 HOH HOH . 
T 5 HOH A 67 1267 31 HOH HOH . 
T 5 HOH A 68 1268 83 HOH HOH . 
T 5 HOH A 69 1269 65 HOH HOH . 
T 5 HOH A 70 1270 71 HOH HOH . 
T 5 HOH A 71 1271 18 HOH HOH . 
T 5 HOH A 72 1272 61 HOH HOH . 
T 5 HOH A 73 1273 40 HOH HOH . 
T 5 HOH A 74 1274 12 HOH HOH . 
T 5 HOH A 75 1275 100 HOH HOH . 
T 5 HOH A 76 1276 81 HOH HOH . 
T 5 HOH A 77 1277 77 HOH HOH . 
T 5 HOH A 78 1278 11 HOH HOH . 
T 5 HOH A 79 1279 105 HOH HOH . 
T 5 HOH A 80 1280 62 HOH HOH . 
T 5 HOH A 81 1281 102 HOH HOH . 
T 5 HOH A 82 1282 46 HOH HOH . 
T 5 HOH A 83 1283 86 HOH HOH . 
T 5 HOH A 84 1284 17 HOH HOH . 
T 5 HOH A 85 1285 54 HOH HOH . 
T 5 HOH A 86 1286 55 HOH HOH . 
T 5 HOH A 87 1287 36 HOH HOH . 
T 5 HOH A 88 1288 64 HOH HOH . 
T 5 HOH A 89 1289 91 HOH HOH . 
T 5 HOH A 90 1290 95 HOH HOH . 
T 5 HOH A 91 1291 53 HOH HOH . 
T 5 HOH A 92 1292 24 HOH HOH . 
T 5 HOH A 93 1293 41 HOH HOH . 
T 5 HOH A 94 1294 47 HOH HOH . 
T 5 HOH A 95 1295 82 HOH HOH . 
T 5 HOH A 96 1296 68 HOH HOH . 
T 5 HOH A 97 1297 48 HOH HOH . 
T 5 HOH A 98 1298 67 HOH HOH . 
T 5 HOH A 99 1299 29 HOH HOH . 
T 5 HOH A 100 1300 34 HOH HOH . 
T 5 HOH A 101 1301 49 HOH HOH . 
T 5 HOH A 102 1302 72 HOH HOH . 
T 5 HOH A 103 1303 94 HOH HOH . 
T 5 HOH A 104 1304 23 HOH HOH . 
T 5 HOH A 105 1305 15 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 . . . N 3 -31.207 33.329 33.249 1 109.22 ? C1 GOL 1113 A 1 
HETATM 2 O O1 GOL . . . N 3 -31.52 34.718 33.172 1 93.92 ? O1 GOL 1113 A 1 
HETATM 3 C C2 GOL . . . N 3 -31.491 32.609 31.943 1 117.79 ? C2 GOL 1113 A 1 
HETATM 4 O O2 GOL . . . N 3 -31.037 31.259 32.039 1 135.58 ? O2 GOL 1113 A 1 
HETATM 5 C C3 GOL . . . N 3 -32.952 32.631 31.534 1 108.33 ? C3 GOL 1113 A 1 
HETATM 6 O O3 GOL . . . N 3 -33.24 31.709 30.48 1 91.23 ? O3 GOL 1113 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           306 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           6 
#