data_7ES2 # _model_server_result.job_id hDVfBB6VEpg3SofmmUOG3g _model_server_result.datetime_utc '2024-10-20 01:31:50' _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 7es2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 7ES2 # _exptl.entry_id 7ES2 _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 90 _cell.angle_gamma 90 _cell.entry_id 7ES2 _cell.length_a 54.444 _cell.length_b 83.496 _cell.length_c 110.645 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ES2 _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 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 524 n n N1 C6 UDP sing 525 n n N1 C1' UDP sing 526 n n C2 N3 UDP sing 527 n n C2 O2 UDP doub 528 n n N3 C4 UDP sing 529 n n N3 HN3 UDP sing 530 n n C4 C5 UDP sing 531 n n C4 O4 UDP doub 532 n n C5 C6 UDP doub 533 n n C5 H5 UDP sing 534 n n C6 H6 UDP sing 535 n n C1' C2' UDP sing 536 n n C1' O4' UDP sing 537 n n C1' H1' UDP sing 538 n n C2' O2' UDP sing 539 n n C2' C3' UDP sing 540 n n C2' H2' UDP sing 541 n n O2' HO2' UDP sing 542 n n C3' C4' UDP sing 543 n n C3' O3' UDP sing 544 n n C3' H3' UDP sing 545 n n C4' O4' UDP sing 546 n n C4' C5' UDP sing 547 n n C4' H4' UDP sing 548 n n O3' HO3' UDP sing 549 n n C5' O5' UDP sing 550 n n C5' "H5'1" UDP sing 551 n n C5' "H5'2" UDP sing 552 n n O5' PA UDP sing 553 n n PA O1A UDP doub 554 n n PA O2A UDP sing 555 n n PA O3A UDP sing 556 n n O2A HOA2 UDP sing 557 n n O3A PB UDP sing 558 n n PB O1B UDP doub 559 n n PB O2B UDP sing 560 n n PB O3B UDP sing 561 n n O2B HOB2 UDP sing 562 n n O3B HOB3 UDP sing 563 n n # _atom_sites.entry_id 7ES2 _atom_sites.fract_transf_matrix[1][1] 0.018367 _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] 0.011977 _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] 0.009038 _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 JDO A 1 502 601 JDO RD5 . D 4 HOH A 1 601 4 HOH HOH . D 4 HOH A 2 602 35 HOH HOH . D 4 HOH A 3 603 26 HOH HOH . D 4 HOH A 4 604 5 HOH HOH . D 4 HOH A 5 605 56 HOH HOH . D 4 HOH A 6 606 22 HOH HOH . D 4 HOH A 7 607 30 HOH HOH . D 4 HOH A 8 608 12 HOH HOH . D 4 HOH A 9 609 29 HOH HOH . D 4 HOH A 10 610 10 HOH HOH . D 4 HOH A 11 611 62 HOH HOH . D 4 HOH A 12 612 17 HOH HOH . D 4 HOH A 13 613 13 HOH HOH . D 4 HOH A 14 614 51 HOH HOH . D 4 HOH A 15 615 2 HOH HOH . D 4 HOH A 16 616 32 HOH HOH . D 4 HOH A 17 617 27 HOH HOH . D 4 HOH A 18 618 67 HOH HOH . D 4 HOH A 19 619 68 HOH HOH . D 4 HOH A 20 620 6 HOH HOH . D 4 HOH A 21 621 11 HOH HOH . D 4 HOH A 22 622 53 HOH HOH . D 4 HOH A 23 623 73 HOH HOH . D 4 HOH A 24 624 75 HOH HOH . D 4 HOH A 25 625 31 HOH HOH . D 4 HOH A 26 626 58 HOH HOH . D 4 HOH A 27 627 1 HOH HOH . D 4 HOH A 28 628 50 HOH HOH . D 4 HOH A 29 629 45 HOH HOH . D 4 HOH A 30 630 46 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 -9.303 12.756 -14.324 1 54.07 0 N1 UDP 501 A 1 HETATM 2 C C2 UDP . . . B 2 -8.991 13.667 -13.286 1 53.55 0 C2 UDP 501 A 1 HETATM 3 N N3 UDP . . . B 2 -9.737 13.698 -12.169 1 57.73 0 N3 UDP 501 A 1 HETATM 4 C C4 UDP . . . B 2 -10.79 12.879 -12.019 1 62.12 0 C4 UDP 501 A 1 HETATM 5 C C5 UDP . . . B 2 -11.123 11.978 -13.022 1 65.71 0 C5 UDP 501 A 1 HETATM 6 C C6 UDP . . . B 2 -10.36 11.938 -14.183 1 67.76 0 C6 UDP 501 A 1 HETATM 7 O O2 UDP . . . B 2 -8.015 14.443 -13.403 1 44.51 0 O2 UDP 501 A 1 HETATM 8 O O4 UDP . . . B 2 -11.477 12.918 -10.979 1 53.66 0 O4 UDP 501 A 1 HETATM 9 C C1' UDP . . . B 2 -8.501 12.741 -15.56 1 43.96 0 C1' UDP 501 A 1 HETATM 10 C C2' UDP . . . B 2 -7.343 11.765 -15.542 1 43.61 0 C2' UDP 501 A 1 HETATM 11 O O2' UDP . . . B 2 -6.154 12.359 -15.021 1 33.76 0 O2' UDP 501 A 1 HETATM 12 C C3' UDP . . . B 2 -7.195 11.379 -16.999 1 46.08 0 C3' UDP 501 A 1 HETATM 13 C C4' UDP . . . B 2 -8.583 11.557 -17.592 1 45.75 0 C4' UDP 501 A 1 HETATM 14 O O4' UDP . . . B 2 -9.317 12.384 -16.685 1 45.3 0 O4' UDP 501 A 1 HETATM 15 O O3' UDP . . . B 2 -6.274 12.248 -17.663 1 39.85 0 O3' UDP 501 A 1 HETATM 16 C C5' UDP . . . B 2 -9.31 10.229 -17.766 1 49.64 0 C5' UDP 501 A 1 HETATM 17 O O5' UDP . . . B 2 -8.756 9.52 -18.873 1 51.17 0 O5' UDP 501 A 1 HETATM 18 P PA UDP . . . B 2 -8.64 7.914 -18.892 1 43.56 0 PA UDP 501 A 1 HETATM 19 O O1A UDP . . . B 2 -8.346 7.464 -20.301 1 52.94 0 O1A UDP 501 A 1 HETATM 20 O O2A UDP . . . B 2 -7.659 7.515 -17.82 1 37.46 0 O2A UDP 501 A 1 HETATM 21 O O3A UDP . . . B 2 -10.117 7.444 -18.459 1 37.43 0 O3A UDP 501 A 1 HETATM 22 P PB UDP . . . B 2 -11.486 7.795 -19.234 1 43.35 0 PB UDP 501 A 1 HETATM 23 O O1B UDP . . . B 2 -11.066 8.117 -20.642 1 54.55 0 O1B UDP 501 A 1 HETATM 24 O O2B UDP . . . B 2 -12.322 6.545 -19.119 1 56.2 0 O2B UDP 501 A 1 HETATM 25 O O3B UDP . . . B 2 -12.086 8.947 -18.47 1 45.52 0 O3B UDP 501 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 25 #