data_6L5P # _model_server_result.job_id Zj5pZVLKeyofx3tN982fyg _model_server_result.datetime_utc '2024-10-19 22:40:07' _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 6l5p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6L5P # _exptl.entry_id 6L5P _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 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 90 _cell.entry_id 6L5P _cell.length_a 87.178 _cell.length_b 139.468 _cell.length_c 73.892 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6L5P _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 6L5P _atom_sites.fract_transf_matrix[1][1] 0.011471 _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] 0.00717 _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] 0.013533 _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 UPG A 1 501 501 UPG UPG . C 3 HOH A 1 601 44 HOH HOH . C 3 HOH A 2 602 33 HOH HOH . C 3 HOH A 3 603 23 HOH HOH . C 3 HOH A 4 604 40 HOH HOH . C 3 HOH A 5 605 34 HOH HOH . C 3 HOH A 6 606 11 HOH HOH . C 3 HOH A 7 607 36 HOH HOH . C 3 HOH A 8 608 14 HOH HOH . C 3 HOH A 9 609 20 HOH HOH . C 3 HOH A 10 610 10 HOH HOH . C 3 HOH A 11 611 18 HOH HOH . C 3 HOH A 12 612 12 HOH HOH . C 3 HOH A 13 613 43 HOH HOH . C 3 HOH A 14 614 8 HOH HOH . C 3 HOH A 15 615 6 HOH HOH . C 3 HOH A 16 616 29 HOH HOH . C 3 HOH A 17 617 41 HOH HOH . C 3 HOH A 18 618 13 HOH HOH . C 3 HOH A 19 619 38 HOH HOH . C 3 HOH A 20 620 5 HOH HOH . C 3 HOH A 21 621 42 HOH HOH . C 3 HOH A 22 622 4 HOH HOH . C 3 HOH A 23 623 9 HOH HOH . C 3 HOH A 24 624 7 HOH HOH . C 3 HOH A 25 625 37 HOH HOH . C 3 HOH A 26 626 28 HOH HOH . C 3 HOH A 27 627 30 HOH HOH . C 3 HOH A 28 628 25 HOH HOH . C 3 HOH A 29 629 46 HOH HOH . C 3 HOH A 30 630 17 HOH HOH . C 3 HOH A 31 631 45 HOH HOH . C 3 HOH A 32 632 27 HOH HOH . C 3 HOH A 33 633 21 HOH HOH . C 3 HOH A 34 634 19 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 . . . B 2 -17.913 -16.604 -21.176 1 23.24 ? N1 UPG 501 A 1 HETATM 2 C C2 UPG . . . B 2 -16.909 -16.592 -22.127 1 25.01 ? C2 UPG 501 A 1 HETATM 3 N N3 UPG . . . B 2 -17.183 -15.846 -23.245 1 25.58 ? N3 UPG 501 A 1 HETATM 4 C C4 UPG . . . B 2 -18.331 -15.122 -23.502 1 25.75 ? C4 UPG 501 A 1 HETATM 5 C C5 UPG . . . B 2 -19.323 -15.183 -22.467 1 25.07 ? C5 UPG 501 A 1 HETATM 6 C C6 UPG . . . B 2 -19.083 -15.907 -21.363 1 24.02 ? C6 UPG 501 A 1 HETATM 7 O O2 UPG . . . B 2 -15.857 -17.204 -21.99 1 25.4 ? O2 UPG 501 A 1 HETATM 8 O O4 UPG . . . B 2 -18.428 -14.497 -24.558 1 25.84 ? O4 UPG 501 A 1 HETATM 9 C C1C UPG . . . B 2 -17.676 -17.395 -19.953 1 23.03 ? C1C UPG 501 A 1 HETATM 10 C C2C UPG . . . B 2 -17.273 -16.561 -18.739 1 22.1 ? C2C UPG 501 A 1 HETATM 11 O O2C UPG . . . B 2 -15.91 -16.195 -18.778 1 20.56 ? O2C UPG 501 A 1 HETATM 12 C C3C UPG . . . B 2 -17.638 -17.556 -17.635 1 21.08 ? C3C UPG 501 A 1 HETATM 13 C C4C UPG . . . B 2 -19.003 -18.044 -18.14 1 22.83 ? C4C UPG 501 A 1 HETATM 14 O O4C UPG . . . B 2 -18.867 -18.06 -19.587 1 24.23 ? O4C UPG 501 A 1 HETATM 15 O O3C UPG . . . B 2 -16.704 -18.627 -17.625 1 22.37 ? O3C UPG 501 A 1 HETATM 16 C C5C UPG . . . B 2 -20.178 -17.177 -17.764 1 26.08 ? C5C UPG 501 A 1 HETATM 17 O O5C UPG . . . B 2 -20.424 -17.308 -16.343 1 28.65 ? O5C UPG 501 A 1 HETATM 18 P PA UPG . . . B 2 -21.134 -16.102 -15.56 1 29.76 ? PA UPG 501 A 1 HETATM 19 O O1A UPG . . . B 2 -20.286 -14.879 -15.67 1 30.83 ? O1A UPG 501 A 1 HETATM 20 O O2A UPG . . . B 2 -21.519 -16.566 -14.194 1 32.99 ? O2A UPG 501 A 1 HETATM 21 O O3A UPG . . . B 2 -22.468 -15.877 -16.424 1 27.99 ? O3A UPG 501 A 1 HETATM 22 P PB UPG . . . B 2 -23.819 -16.724 -16.588 1 22.96 ? PB UPG 501 A 1 HETATM 23 O O1B UPG . . . B 2 -23.512 -18.014 -17.274 1 24.31 ? O1B UPG 501 A 1 HETATM 24 O O2B UPG . . . B 2 -24.884 -15.848 -17.16 1 26 ? O2B UPG 501 A 1 HETATM 25 O O3B UPG . . . B 2 -24.143 -17.016 -15.045 1 24.19 ? O3B UPG 501 A 1 HETATM 26 C C1' UPG . . . B 2 -25.283 -17.689 -14.583 1 24.71 ? C1' UPG 501 A 1 HETATM 27 C C2' UPG . . . B 2 -26.25 -16.657 -14.02 1 25.23 ? C2' UPG 501 A 1 HETATM 28 C C3' UPG . . . B 2 -25.626 -15.959 -12.823 1 21.07 ? C3' UPG 501 A 1 HETATM 29 C C4' UPG . . . B 2 -25.138 -16.978 -11.807 1 21.15 ? C4' UPG 501 A 1 HETATM 30 C C5' UPG . . . B 2 -24.211 -17.984 -12.478 1 22.12 ? C5' UPG 501 A 1 HETATM 31 C C6' UPG . . . B 2 -23.765 -19.089 -11.551 1 23.19 ? C6' UPG 501 A 1 HETATM 32 O O2' UPG . . . B 2 -26.616 -15.722 -15.031 1 30.05 ? O2' UPG 501 A 1 HETATM 33 O O3' UPG . . . B 2 -26.576 -15.077 -12.226 1 17.48 ? O3' UPG 501 A 1 HETATM 34 O O4' UPG . . . B 2 -24.44 -16.326 -10.75 1 22.6 ? O4' UPG 501 A 1 HETATM 35 O O5' UPG . . . B 2 -24.907 -18.609 -13.573 1 24.23 ? O5' UPG 501 A 1 HETATM 36 O O6' UPG . . . B 2 -24.876 -19.838 -11.065 1 25.78 ? O6' UPG 501 A 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 261 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 36 #