data_7XX4 # _model_server_result.job_id fyzmpmQYRm_C4ZkgtZUHZQ _model_server_result.datetime_utc '2024-12-27 12:02:26' _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 7xx4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 7XX4 # _exptl.entry_id 7XX4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _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 7XX4 _cell.length_a 65.716 _cell.length_b 92.285 _cell.length_c 191.438 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7XX4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1 B,D,F 2 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 'C15 H24 N2 O17 P2' _chem_comp.formula_weight 566.302 _chem_comp.id UPG _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER" # 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 N1 C2 UPG sing 358 n n N1 C6 UPG sing 359 n n N1 C1C UPG sing 360 n n C2 N3 UPG sing 361 n n C2 O2 UPG doub 362 n n N3 C4 UPG sing 363 n n N3 HN3 UPG sing 364 n n C4 C5 UPG sing 365 n n C4 O4 UPG doub 366 n n C5 C6 UPG doub 367 n n C5 H5 UPG sing 368 n n C6 H6 UPG sing 369 n n C1C C2C UPG sing 370 n n C1C O4C UPG sing 371 n n C1C H1C UPG sing 372 n n C2C O2C UPG sing 373 n n C2C C3C UPG sing 374 n n C2C H2C UPG sing 375 n n O2C HO2C UPG sing 376 n n C3C C4C UPG sing 377 n n C3C O3C UPG sing 378 n n C3C H3C UPG sing 379 n n C4C O4C UPG sing 380 n n C4C C5C UPG sing 381 n n C4C H4C UPG sing 382 n n O3C HO3C UPG sing 383 n n C5C O5C UPG sing 384 n n C5C H5C1 UPG sing 385 n n C5C H5C2 UPG sing 386 n n O5C PA UPG sing 387 n n PA O1A UPG doub 388 n n PA O2A UPG sing 389 n n PA O3A UPG sing 390 n n O2A HOA2 UPG sing 391 n n O3A PB UPG sing 392 n n PB O1B UPG doub 393 n n PB O2B UPG sing 394 n n PB O3B UPG sing 395 n n O2B HOB2 UPG sing 396 n n O3B C1' UPG sing 397 n n C1' C2' UPG sing 398 n n C1' O5' UPG sing 399 n n C1' H1' UPG sing 400 n n C2' C3' UPG sing 401 n n C2' O2' UPG sing 402 n n C2' H2' UPG sing 403 n n C3' C4' UPG sing 404 n n C3' O3' UPG sing 405 n n C3' H3' UPG sing 406 n n C4' C5' UPG sing 407 n n C4' O4' UPG sing 408 n n C4' H4' UPG sing 409 n n C5' C6' UPG sing 410 n n C5' O5' UPG sing 411 n n C5' H5' UPG sing 412 n n C6' O6' UPG sing 413 n n C6' "H6'1" UPG sing 414 n n C6' "H6'2" UPG sing 415 n n O2' HO2' UPG sing 416 n n O3' HO3' UPG sing 417 n n O4' HO4' UPG sing 418 n n O6' HO6' UPG sing 419 n n # _atom_sites.entry_id 7XX4 _atom_sites.fract_transf_matrix[1][1] 0.015217 _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] 0.010836 _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] 0.005224 _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 UPG A 1 501 1 UPG LIG . D 2 UPG B 1 501 2 UPG LIG . E 3 HOH A 1 601 2 HOH HOH . E 3 HOH A 2 602 4 HOH HOH . E 3 HOH A 3 603 14 HOH HOH . E 3 HOH A 4 604 16 HOH HOH . E 3 HOH A 5 605 5 HOH HOH . E 3 HOH A 6 606 6 HOH HOH . E 3 HOH A 7 607 9 HOH HOH . E 3 HOH A 8 608 3 HOH HOH . E 3 HOH A 9 609 18 HOH HOH . E 3 HOH A 10 610 17 HOH HOH . E 3 HOH A 11 611 15 HOH HOH . E 3 HOH A 12 612 19 HOH HOH . F 3 HOH B 1 601 11 HOH HOH . F 3 HOH B 2 602 1 HOH HOH . F 3 HOH B 3 603 13 HOH HOH . F 3 HOH B 4 604 12 HOH HOH . F 3 HOH B 5 605 7 HOH HOH . F 3 HOH B 6 606 8 HOH HOH . F 3 HOH B 7 607 10 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 N N1 UPG . . . C 2 -11.334 -16.776 7.26 1 55.88 ? N1 UPG 501 A 1 HETATM 2 C C2 UPG . . . C 2 -12.145 -15.779 6.665 1 55.91 ? C2 UPG 501 A 1 HETATM 3 N N3 UPG . . . C 2 -11.544 -14.626 6.064 1 53.47 ? N3 UPG 501 A 1 HETATM 4 C C4 UPG . . . C 2 -10.144 -14.45 6.072 1 56.11 ? C4 UPG 501 A 1 HETATM 5 C C5 UPG . . . C 2 -9.331 -15.502 6.706 1 51.5 ? C5 UPG 501 A 1 HETATM 6 C C6 UPG . . . C 2 -9.935 -16.598 7.26 1 51.51 ? C6 UPG 501 A 1 HETATM 7 O O2 UPG . . . C 2 -13.362 -15.902 6.653 1 60.36 ? O2 UPG 501 A 1 HETATM 8 O O4 UPG . . . C 2 -9.69 -13.426 5.542 1 64.11 ? O4 UPG 501 A 1 HETATM 9 C C1C UPG . . . C 2 -12.057 -18.013 7.895 1 53.07 ? C1C UPG 501 A 1 HETATM 10 C C2C UPG . . . C 2 -11.936 -19.327 7.074 1 57.61 ? C2C UPG 501 A 1 HETATM 11 O O2C UPG . . . C 2 -12.968 -19.391 6.148 1 61.53 ? O2C UPG 501 A 1 HETATM 12 C C3C UPG . . . C 2 -12.173 -20.415 8.163 1 63.17 ? C3C UPG 501 A 1 HETATM 13 C C4C UPG . . . C 2 -11.626 -19.732 9.414 1 57.54 ? C4C UPG 501 A 1 HETATM 14 O O4C UPG . . . C 2 -11.427 -18.344 9.094 1 61.77 ? O4C UPG 501 A 1 HETATM 15 O O3C UPG . . . C 2 -13.508 -20.723 8.436 1 60.42 ? O3C UPG 501 A 1 HETATM 16 C C5C UPG . . . C 2 -10.298 -20.422 9.82 1 54.29 ? C5C UPG 501 A 1 HETATM 17 O O5C UPG . . . C 2 -10.23 -21.638 9.272 1 72.46 ? O5C UPG 501 A 1 HETATM 18 P PA UPG . . . C 2 -8.842 -22.653 9.693 1 65.85 ? PA UPG 501 A 1 HETATM 19 O O1A UPG . . . C 2 -8.023 -22.374 8.497 1 71.64 ? O1A UPG 501 A 1 HETATM 20 O O2A UPG . . . C 2 -9.333 -24.034 9.932 1 69.83 ? O2A UPG 501 A 1 HETATM 21 O O3A UPG . . . C 2 -8.232 -21.931 11.012 1 72.27 ? O3A UPG 501 A 1 HETATM 22 P PB UPG . . . C 2 -6.763 -21.244 11.189 1 66.77 ? PB UPG 501 A 1 HETATM 23 O O1B UPG . . . C 2 -6.8 -19.793 11.457 1 67.64 ? O1B UPG 501 A 1 HETATM 24 O O2B UPG . . . C 2 -5.943 -21.739 10.062 1 79.57 ? O2B UPG 501 A 1 HETATM 25 O O3B UPG . . . C 2 -5.787 -22.02 12.539 1 104.53 ? O3B UPG 501 A 1 HETATM 26 C C1' UPG . . . C 2 -5.984 -22.027 13.875 1 115.01 ? C1' UPG 501 A 1 HETATM 27 C C2' UPG . . . C 2 -4.634 -21.571 14.478 1 114.13 ? C2' UPG 501 A 1 HETATM 28 C C3' UPG . . . C 2 -4.909 -21.434 15.976 1 104.65 ? C3' UPG 501 A 1 HETATM 29 C C4' UPG . . . C 2 -4.909 -22.872 16.568 1 97.89 ? C4' UPG 501 A 1 HETATM 30 C C5' UPG . . . C 2 -5.987 -23.733 15.782 1 98.01 ? C5' UPG 501 A 1 HETATM 31 C C6' UPG . . . C 2 -7.216 -23.816 16.701 1 91.11 ? C6' UPG 501 A 1 HETATM 32 O O2' UPG . . . C 2 -3.713 -22.583 14.258 1 120.75 ? O2' UPG 501 A 1 HETATM 33 O O3' UPG . . . C 2 -6.189 -20.856 16.094 1 95.77 ? O3' UPG 501 A 1 HETATM 34 O O4' UPG . . . C 2 -3.63 -23.445 16.481 1 89.57 ? O4' UPG 501 A 1 HETATM 35 O O5' UPG . . . C 2 -6.276 -23.352 14.432 1 111.85 ? O5' UPG 501 A 1 HETATM 36 O O6' UPG . . . C 2 -6.921 -23.371 18.003 1 78.61 ? O6' UPG 501 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 365 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #