data_5YQZ # _model_server_result.job_id lAzGdXr7_nNoTibIy-SF1A _model_server_result.datetime_utc '2024-11-14 06:52:51' _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 5yqz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1206}' # _entry.id 5YQZ # _exptl.entry_id 5YQZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 356.54 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate' _entity.pdbx_number_of_molecules 6 _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 5YQZ _cell.length_a 60.12 _cell.length_b 108.79 _cell.length_c 216.25 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YQZ _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 ? 4 E N N ? 4 F N N ? 4 G N N ? 4 H N N ? 4 I N N ? 4 J N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n C NAG 1 A 1 NAG R 501 NAG 3 n C NAG 2 A 2 NAG R 502 NAG 3 n D NAG 1 B 1 NAG R 503 NAG 3 n D NAG 2 B 2 NAG R 504 NAG # 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 20 R CYS 43 1_555 A SG CYS 44 R CYS 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 35 R CYS 58 1_555 A SG CYS 77 R CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 58 R CYS 81 1_555 A SG CYS 98 R CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf4 A SG CYS 201 R CYS 224 1_555 A SG CYS 429 R CYS 294 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? covale ? covale1 A ND2 ASN 36 R ASN 59 1_555 C C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale2 A ND2 ASN 55 R ASN 78 1_555 D C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 C O4 NAG . A NAG 1 1_555 C C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale4 D O4 NAG . B NAG 1 1_555 D C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? # _chem_comp.formula 'C21 H40 O4' _chem_comp.formula_weight 356.54 _chem_comp.id OLC _chem_comp.mon_nstd_flag . _chem_comp.name '(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1-Oleoyl-R-glycerol # 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 C18 C17 OLC sing 265 n n C10 C9 OLC doub 266 n n C10 C11 OLC sing 267 n n C9 C8 OLC sing 268 n n C17 C16 OLC sing 269 z n C11 C12 OLC sing 270 n n C8 C7 OLC sing 271 n n C24 C22 OLC sing 272 n n C24 O25 OLC sing 273 n n C16 C15 OLC sing 274 n n C12 C13 OLC sing 275 n n C7 C6 OLC sing 276 n n C15 C14 OLC sing 277 n n C13 C14 OLC sing 278 n n C6 C5 OLC sing 279 n n C5 C4 OLC sing 280 n n C4 C3 OLC sing 281 n n C3 C2 OLC sing 282 n n C2 C1 OLC sing 283 n n C21 C22 OLC sing 284 n n C21 O20 OLC sing 285 n n C1 O19 OLC doub 286 n n C1 O20 OLC sing 287 n n C22 O23 OLC sing 288 n n C18 H18 OLC sing 289 n n C18 H18A OLC sing 290 n n C18 H18B OLC sing 291 n n C10 H10 OLC sing 292 n n C9 H9 OLC sing 293 n n C17 H17 OLC sing 294 n n C17 H17A OLC sing 295 n n C11 H11 OLC sing 296 n n C11 H11A OLC sing 297 n n C8 H8 OLC sing 298 n n C8 H8A OLC sing 299 n n C24 H24 OLC sing 300 n n C24 H24A OLC sing 301 n n C16 H16 OLC sing 302 n n C16 H16A OLC sing 303 n n C12 H12 OLC sing 304 n n C12 H12A OLC sing 305 n n C7 H7 OLC sing 306 n n C7 H7A OLC sing 307 n n C15 H15 OLC sing 308 n n C15 H15A OLC sing 309 n n C13 H13 OLC sing 310 n n C13 H13A OLC sing 311 n n C6 H6 OLC sing 312 n n C6 H6A OLC sing 313 n n C14 H14 OLC sing 314 n n C14 H14A OLC sing 315 n n C5 H5 OLC sing 316 n n C5 H5A OLC sing 317 n n C4 H4 OLC sing 318 n n C4 H4A OLC sing 319 n n C3 H3 OLC sing 320 n n C3 H3A OLC sing 321 n n C2 H2 OLC sing 322 n n C2 H2A OLC sing 323 n n C21 H21 OLC sing 324 n n C21 H21A OLC sing 325 n n C22 H22 OLC sing 326 n n O25 HO25 OLC sing 327 n n O23 HO23 OLC sing 328 n n # _atom_sites.entry_id 5YQZ _atom_sites.fract_transf_matrix[1][1] 0.016633 _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] 0.009192 _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] 0.004624 _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 E 4 OLC R 1 1205 505 OLC OLC . F 4 OLC R 1 1206 506 OLC OLC . G 4 OLC R 1 1207 507 OLC OLC . H 4 OLC R 1 1208 508 OLC OLC . I 4 OLC R 1 1209 509 OLC OLC . J 4 OLC R 1 1210 510 OLC OLC . K 5 PO4 R 1 1211 201 PO4 PO4 . # 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 C24 OLC . . . F 4 -22.593 7.67 11.025 1 142.87 ? C24 OLC 1206 R 1 HETATM 2 C C6 OLC . . . F 4 -22.757 5.662 0.816 1 127.71 ? C6 OLC 1206 R 1 HETATM 3 C C5 OLC . . . F 4 -22.159 5.812 2.215 1 128.63 ? C5 OLC 1206 R 1 HETATM 4 C C4 OLC . . . F 4 -23.296 5.85 3.231 1 131 ? C4 OLC 1206 R 1 HETATM 5 C C3 OLC . . . F 4 -22.709 5.991 4.622 1 134.15 ? C3 OLC 1206 R 1 HETATM 6 C C2 OLC . . . F 4 -23.706 5.371 5.594 1 138.25 ? C2 OLC 1206 R 1 HETATM 7 C C21 OLC . . . F 4 -22.463 7.337 8.487 1 144.35 ? C21 OLC 1206 R 1 HETATM 8 C C1 OLC . . . F 4 -23.142 5.538 7.005 1 142.42 ? C1 OLC 1206 R 1 HETATM 9 C C22 OLC . . . F 4 -22.453 6.664 9.889 1 144.46 ? C22 OLC 1206 R 1 HETATM 10 O O19 OLC . . . F 4 -22.568 4.611 7.572 1 143.96 ? O19 OLC 1206 R 1 HETATM 11 O O25 OLC . . . F 4 -21.318 8.228 11.363 1 141.29 ? O25 OLC 1206 R 1 HETATM 12 O O23 OLC . . . F 4 -23.468 5.661 10.049 1 145.06 ? O23 OLC 1206 R 1 HETATM 13 O O20 OLC . . . F 4 -23.432 6.748 7.57 1 143.72 ? O20 OLC 1206 R 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 13 #