data_7W0Z # _model_server_result.job_id E126WPmtdh_Pr55wf3JFPw _model_server_result.datetime_utc '2024-11-05 21:07:07' _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 7w0z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 7W0Z # _exptl.entry_id 7W0Z _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 96.92 _cell.angle_gamma 90 _cell.entry_id 7W0Z _cell.length_a 51.026 _cell.length_b 76.553 _cell.length_c 63.553 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7W0Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _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 _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 423 n n N1 C6 UDP sing 424 n n N1 C1' UDP sing 425 n n C2 N3 UDP sing 426 n n C2 O2 UDP doub 427 n n N3 C4 UDP sing 428 n n N3 HN3 UDP sing 429 n n C4 C5 UDP sing 430 n n C4 O4 UDP doub 431 n n C5 C6 UDP doub 432 n n C5 H5 UDP sing 433 n n C6 H6 UDP sing 434 n n C1' C2' UDP sing 435 n n C1' O4' UDP sing 436 n n C1' H1' UDP sing 437 n n C2' O2' UDP sing 438 n n C2' C3' UDP sing 439 n n C2' H2' UDP sing 440 n n O2' HO2' UDP sing 441 n n C3' C4' UDP sing 442 n n C3' O3' UDP sing 443 n n C3' H3' UDP sing 444 n n C4' O4' UDP sing 445 n n C4' C5' UDP sing 446 n n C4' H4' UDP sing 447 n n O3' HO3' UDP sing 448 n n C5' O5' UDP sing 449 n n C5' "H5'1" UDP sing 450 n n C5' "H5'2" UDP sing 451 n n O5' PA UDP sing 452 n n PA O1A UDP doub 453 n n PA O2A UDP sing 454 n n PA O3A UDP sing 455 n n O2A HOA2 UDP sing 456 n n O3A PB UDP sing 457 n n PB O1B UDP doub 458 n n PB O2B UDP sing 459 n n PB O3B UDP sing 460 n n O2B HOB2 UDP sing 461 n n O3B HOB3 UDP sing 462 n n # _atom_sites.entry_id 7W0Z _atom_sites.fract_transf_matrix[1][1] 0.019598 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00238 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013063 _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] 0.01585 _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 6JI A 1 502 502 6JI RES . D 4 HOH A 1 601 43 HOH HOH . D 4 HOH A 2 602 22 HOH HOH . D 4 HOH A 3 603 17 HOH HOH . D 4 HOH A 4 604 37 HOH HOH . D 4 HOH A 5 605 23 HOH HOH . D 4 HOH A 6 606 40 HOH HOH . D 4 HOH A 7 607 2 HOH HOH . D 4 HOH A 8 608 11 HOH HOH . D 4 HOH A 9 609 25 HOH HOH . D 4 HOH A 10 610 3 HOH HOH . D 4 HOH A 11 611 5 HOH HOH . D 4 HOH A 12 612 1 HOH HOH . D 4 HOH A 13 613 6 HOH HOH . D 4 HOH A 14 614 4 HOH HOH . D 4 HOH A 15 615 21 HOH HOH . D 4 HOH A 16 616 18 HOH HOH . D 4 HOH A 17 617 13 HOH HOH . D 4 HOH A 18 618 33 HOH HOH . D 4 HOH A 19 619 77 HOH HOH . D 4 HOH A 20 620 71 HOH HOH . D 4 HOH A 21 621 24 HOH HOH . D 4 HOH A 22 622 20 HOH HOH . D 4 HOH A 23 623 85 HOH HOH . D 4 HOH A 24 624 8 HOH HOH . D 4 HOH A 25 625 42 HOH HOH . D 4 HOH A 26 626 35 HOH HOH . D 4 HOH A 27 627 19 HOH HOH . D 4 HOH A 28 628 98 HOH HOH . D 4 HOH A 29 629 10 HOH HOH . D 4 HOH A 30 630 16 HOH HOH . D 4 HOH A 31 631 36 HOH HOH . D 4 HOH A 32 632 293 HOH HOH . D 4 HOH A 33 633 12 HOH HOH . D 4 HOH A 34 634 7 HOH HOH . D 4 HOH A 35 635 14 HOH HOH . D 4 HOH A 36 636 28 HOH HOH . D 4 HOH A 37 637 272 HOH HOH . D 4 HOH A 38 638 30 HOH HOH . D 4 HOH A 39 639 26 HOH HOH . D 4 HOH A 40 640 39 HOH HOH . D 4 HOH A 41 641 53 HOH HOH . D 4 HOH A 42 642 27 HOH HOH . D 4 HOH A 43 643 45 HOH HOH . D 4 HOH A 44 644 38 HOH HOH . D 4 HOH A 45 645 99 HOH HOH . D 4 HOH A 46 646 34 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 44.486 35.476 41.835 1 17.65 ? N1 UDP 501 A 1 HETATM 2 C C2 UDP . . . B 2 45.385 36.161 41.167 1 17.64 ? C2 UDP 501 A 1 HETATM 3 N N3 UDP . . . B 2 46.058 37.14 41.71 1 17.3 ? N3 UDP 501 A 1 HETATM 4 C C4 UDP . . . B 2 45.843 37.454 42.966 1 16.99 ? C4 UDP 501 A 1 HETATM 5 C C5 UDP . . . B 2 44.898 36.774 43.735 1 17.68 ? C5 UDP 501 A 1 HETATM 6 C C6 UDP . . . B 2 44.202 35.745 43.106 1 17.23 ? C6 UDP 501 A 1 HETATM 7 O O2 UDP . . . B 2 45.639 35.834 39.841 1 14.45 ? O2 UDP 501 A 1 HETATM 8 O O4 UDP . . . B 2 46.584 38.502 43.492 1 18.16 ? O4 UDP 501 A 1 HETATM 9 C C1' UDP . . . B 2 43.779 34.412 41.1 1 17.92 ? C1' UDP 501 A 1 HETATM 10 C C2' UDP . . . B 2 44.198 33.011 41.58 1 18.85 ? C2' UDP 501 A 1 HETATM 11 O O2' UDP . . . B 2 45.249 32.563 40.818 1 16.3 ? O2' UDP 501 A 1 HETATM 12 C C3' UDP . . . B 2 42.905 32.19 41.369 1 15.93 ? C3' UDP 501 A 1 HETATM 13 C C4' UDP . . . B 2 41.911 33.045 41.551 1 16.59 ? C4' UDP 501 A 1 HETATM 14 O O4' UDP . . . B 2 42.481 34.53 41.305 1 17.59 ? O4' UDP 501 A 1 HETATM 15 O O3' UDP . . . B 2 42.89 31.692 39.952 1 19.61 ? O3' UDP 501 A 1 HETATM 16 C C5' UDP . . . B 2 41.327 32.983 42.954 1 16.55 ? C5' UDP 501 A 1 HETATM 17 O O5' UDP . . . B 2 40.304 32.021 42.925 1 14.38 ? O5' UDP 501 A 1 HETATM 18 P PA UDP . . . B 2 40.058 31.09 44.243 1 15.16 ? PA UDP 501 A 1 HETATM 19 O O1A UDP . . . B 2 39.315 29.822 43.871 1 15.29 ? O1A UDP 501 A 1 HETATM 20 O O2A UDP . . . B 2 41.351 30.743 44.932 1 16.32 -1 O2A UDP 501 A 1 HETATM 21 O O3A UDP . . . B 2 39.227 31.981 45.328 1 18.21 ? O3A UDP 501 A 1 HETATM 22 P PB UDP . . . B 2 38.025 33.067 45.026 1 17.81 ? PB UDP 501 A 1 HETATM 23 O O1B UDP . . . B 2 37.093 32.494 43.983 1 16.84 ? O1B UDP 501 A 1 HETATM 24 O O2B UDP . . . B 2 38.598 34.395 44.612 1 17.06 -1 O2B UDP 501 A 1 HETATM 25 O O3B UDP . . . B 2 37.374 33.198 46.391 1 19.04 ? O3B UDP 501 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 25 #