data_7W10 # _model_server_result.job_id jF-NDRYti4yW1PSdXkZV3w _model_server_result.datetime_utc '2024-11-24 14:04:33' _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 7w10 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 7W10 # _exptl.entry_id 7W10 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _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 95.572 _cell.angle_gamma 90 _cell.entry_id 7W10 _cell.length_a 53.178 _cell.length_b 74.64 _cell.length_c 63.609 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7W10 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # _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,D,E _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 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms ? # 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 UDP sing 443 n n N1 C6 UDP sing 444 n n N1 C1' UDP sing 445 n n C2 N3 UDP sing 446 n n C2 O2 UDP doub 447 n n N3 C4 UDP sing 448 n n N3 HN3 UDP sing 449 n n C4 C5 UDP sing 450 n n C4 O4 UDP doub 451 n n C5 C6 UDP doub 452 n n C5 H5 UDP sing 453 n n C6 H6 UDP sing 454 n n C1' C2' UDP sing 455 n n C1' O4' UDP sing 456 n n C1' H1' UDP sing 457 n n C2' O2' UDP sing 458 n n C2' C3' UDP sing 459 n n C2' H2' UDP sing 460 n n O2' HO2' UDP sing 461 n n C3' C4' UDP sing 462 n n C3' O3' UDP sing 463 n n C3' H3' UDP sing 464 n n C4' O4' UDP sing 465 n n C4' C5' UDP sing 466 n n C4' H4' UDP sing 467 n n O3' HO3' UDP sing 468 n n C5' O5' UDP sing 469 n n C5' "H5'1" UDP sing 470 n n C5' "H5'2" UDP sing 471 n n O5' PA UDP sing 472 n n PA O1A UDP doub 473 n n PA O2A UDP sing 474 n n PA O3A UDP sing 475 n n O2A HOA2 UDP sing 476 n n O3A PB UDP sing 477 n n PB O1B UDP doub 478 n n PB O2B UDP sing 479 n n PB O3B UDP sing 480 n n O2B HOB2 UDP sing 481 n n O3B HOB3 UDP sing 482 n n # _atom_sites.entry_id 7W10 _atom_sites.fract_transf_matrix[1][1] 0.018805 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001835 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013398 _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] 0.015796 _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 UDP A 1 501 501 UDP UDP . C 3 TRS A 1 502 701 TRS TRS . D 4 BUF A 1 503 702 BUF BUF . E 5 HOH A 1 601 7 HOH HOH . E 5 HOH A 2 602 3 HOH HOH . E 5 HOH A 3 603 2 HOH HOH . E 5 HOH A 4 604 12 HOH HOH . E 5 HOH A 5 605 10 HOH HOH . E 5 HOH A 6 606 9 HOH HOH . E 5 HOH A 7 607 153 HOH HOH . E 5 HOH A 8 608 5 HOH HOH . E 5 HOH A 9 609 4 HOH HOH . E 5 HOH A 10 610 1 HOH HOH . E 5 HOH A 11 611 14 HOH HOH . E 5 HOH A 12 612 25 HOH HOH . E 5 HOH A 13 613 30 HOH HOH . E 5 HOH A 14 614 46 HOH HOH . E 5 HOH A 15 615 8 HOH HOH . E 5 HOH A 16 616 13 HOH HOH . E 5 HOH A 17 617 16 HOH HOH . E 5 HOH A 18 618 39 HOH HOH . E 5 HOH A 19 619 23 HOH HOH . E 5 HOH A 20 620 21 HOH HOH . E 5 HOH A 21 621 92 HOH HOH . E 5 HOH A 22 622 20 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 UDP . . . B 2 -24.211 -2.392 -10.228 1 32.29 ? N1 UDP 501 A 1 HETATM 2 C C2 UDP . . . B 2 -25.288 -1.707 -9.443 1 34.9 ? C2 UDP 501 A 1 HETATM 3 N N3 UDP . . . B 2 -26.146 -0.672 -10.11 1 33.34 ? N3 UDP 501 A 1 HETATM 4 C C4 UDP . . . B 2 -25.926 -0.33 -11.52 1 34.11 ? C4 UDP 501 A 1 HETATM 5 C C5 UDP . . . B 2 -24.849 -1.009 -12.297 1 34.53 ? C5 UDP 501 A 1 HETATM 6 C C6 UDP . . . B 2 -24 -2.036 -11.624 1 33.79 ? C6 UDP 501 A 1 HETATM 7 O O2 UDP . . . B 2 -25.475 -1.986 -8.295 1 32.99 ? O2 UDP 501 A 1 HETATM 8 O O4 UDP . . . B 2 -26.599 0.493 -12.055 1 33.35 ? O4 UDP 501 A 1 HETATM 9 C C1' UDP . . . B 2 -23.344 -3.379 -9.577 1 34.4 ? C1' UDP 501 A 1 HETATM 10 C C2' UDP . . . B 2 -23.74 -4.922 -9.879 1 33.64 ? C2' UDP 501 A 1 HETATM 11 O O2' UDP . . . B 2 -24.926 -5.277 -9.096 1 28.4 ? O2' UDP 501 A 1 HETATM 12 C C3' UDP . . . B 2 -22.683 -5.627 -9.526 1 32.8 ? C3' UDP 501 A 1 HETATM 13 C C4' UDP . . . B 2 -21.476 -4.657 -9.565 1 35.67 ? C4' UDP 501 A 1 HETATM 14 O O4' UDP . . . B 2 -22.093 -3.294 -9.976 1 36.73 ? O4' UDP 501 A 1 HETATM 15 O O3' UDP . . . B 2 -22.807 -6.124 -8.113 1 31.86 ? O3' UDP 501 A 1 HETATM 16 C C5' UDP . . . B 2 -20.387 -5.14 -10.348 1 36.53 ? C5' UDP 501 A 1 HETATM 17 O O5' UDP . . . B 2 -20.554 -5.096 -11.728 1 32.43 ? O5' UDP 501 A 1 HETATM 18 P PA UDP . . . B 2 -19.922 -6.249 -12.759 1 32.8 ? PA UDP 501 A 1 HETATM 19 O O1A UDP . . . B 2 -21.006 -6.88 -13.576 1 27.94 ? O1A UDP 501 A 1 HETATM 20 O O2A UDP . . . B 2 -19.131 -7.322 -12.067 1 33.46 -1 O2A UDP 501 A 1 HETATM 21 O O3A UDP . . . B 2 -18.894 -5.547 -13.826 1 33.62 ? O3A UDP 501 A 1 HETATM 22 P PB UDP . . . B 2 -17.887 -4.276 -13.525 1 34.54 ? PB UDP 501 A 1 HETATM 23 O O1B UDP . . . B 2 -17.28 -3.902 -14.887 1 39.47 -1 O1B UDP 501 A 1 HETATM 24 O O2B UDP . . . B 2 -18.644 -3.08 -12.988 1 34.08 ? O2B UDP 501 A 1 HETATM 25 O O3B UDP . . . B 2 -16.812 -4.718 -12.553 1 35.54 ? O3B UDP 501 A 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 41 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 960 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #