data_4YYY # _model_server_result.job_id dygYd58baNnur14J3qWTQA _model_server_result.datetime_utc '2025-01-10 16:44:13' _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 4yyy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":502}' # _entry.id 4YYY # _exptl.entry_id 4YYY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 244.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description URIDINE _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 4YYY _cell.length_a 193.933 _cell.length_b 193.933 _cell.length_c 57.73 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YYY _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression B,F,G,H,J 1 1 A,C,D,E,I 1 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 1_554 x,y,z-1 1 0 0 0 1 0 0 0 1 0 0 -57.73 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 G N N # _chem_comp.formula 'C9 H12 N2 O6' _chem_comp.formula_weight 244.201 _chem_comp.id URI _chem_comp.mon_nstd_flag . _chem_comp.name URIDINE _chem_comp.type non-polymer _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 URI sing 401 n n N1 C6 URI sing 402 n n N1 C1' URI sing 403 n n C2 N3 URI sing 404 n n C2 O2 URI doub 405 n n N3 C4 URI sing 406 n n N3 H3 URI sing 407 n n C4 C5 URI sing 408 n n C4 O4 URI doub 409 n n C5 C6 URI doub 410 n n C5 H5 URI sing 411 n n C6 H6 URI sing 412 n n C1' C2' URI sing 413 n n C1' O4' URI sing 414 n n C1' H1' URI sing 415 n n C2' C3' URI sing 416 n n C2' O2' URI sing 417 n n C2' H2' URI sing 418 n n C3' C4' URI sing 419 n n C3' O3' URI sing 420 n n C3' H3' URI sing 421 n n C4' O4' URI sing 422 n n C4' C5' URI sing 423 n n C4' H4' URI sing 424 n n O2' HO2' URI sing 425 n n O3' HO3' URI sing 426 n n C5' O5' URI sing 427 n n C5' "H5'1" URI sing 428 n n C5' "H5'2" URI sing 429 n n O5' HO5' URI sing 430 n n # _atom_sites.entry_id 4YYY _atom_sites.fract_transf_matrix[1][1] 0.005156 _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] 0.005156 _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] 0.017322 _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 CIT A 1 501 1 CIT CIT . D 2 CIT A 1 502 3 CIT CIT . E 3 PGE A 1 503 1 PGE PGE . F 4 URI B 1 501 1 URI URI . G 4 URI B 1 502 2 URI URI . H 2 CIT B 1 503 2 CIT CIT . I 5 HOH A 1 601 68 HOH HOH . I 5 HOH A 2 602 55 HOH HOH . I 5 HOH A 3 603 5 HOH HOH . I 5 HOH A 4 604 17 HOH HOH . I 5 HOH A 5 605 70 HOH HOH . I 5 HOH A 6 606 9 HOH HOH . I 5 HOH A 7 607 7 HOH HOH . I 5 HOH A 8 608 10 HOH HOH . I 5 HOH A 9 609 24 HOH HOH . I 5 HOH A 10 610 4 HOH HOH . I 5 HOH A 11 611 15 HOH HOH . I 5 HOH A 12 612 43 HOH HOH . I 5 HOH A 13 613 12 HOH HOH . I 5 HOH A 14 614 64 HOH HOH . I 5 HOH A 15 615 39 HOH HOH . I 5 HOH A 16 616 58 HOH HOH . I 5 HOH A 17 617 38 HOH HOH . I 5 HOH A 18 618 20 HOH HOH . I 5 HOH A 19 619 28 HOH HOH . I 5 HOH A 20 620 37 HOH HOH . I 5 HOH A 21 621 36 HOH HOH . I 5 HOH A 22 622 22 HOH HOH . I 5 HOH A 23 623 72 HOH HOH . I 5 HOH A 24 624 26 HOH HOH . I 5 HOH A 25 625 62 HOH HOH . I 5 HOH A 26 626 21 HOH HOH . I 5 HOH A 27 627 25 HOH HOH . I 5 HOH A 28 628 27 HOH HOH . I 5 HOH A 29 629 71 HOH HOH . J 5 HOH B 1 601 14 HOH HOH . J 5 HOH B 2 602 46 HOH HOH . J 5 HOH B 3 603 32 HOH HOH . J 5 HOH B 4 604 66 HOH HOH . J 5 HOH B 5 605 11 HOH HOH . J 5 HOH B 6 606 6 HOH HOH . J 5 HOH B 7 607 19 HOH HOH . J 5 HOH B 8 608 63 HOH HOH . J 5 HOH B 9 609 42 HOH HOH . J 5 HOH B 10 610 47 HOH HOH . J 5 HOH B 11 611 35 HOH HOH . J 5 HOH B 12 612 44 HOH HOH . J 5 HOH B 13 613 34 HOH HOH . J 5 HOH B 14 614 13 HOH HOH . J 5 HOH B 15 615 69 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 URI . . . G 4 19.226 -48.902 5.21 0.87 89.86 ? N1 URI 502 B 1 HETATM 2 C C2 URI . . . G 4 18.645 -48.522 6.417 0.87 87.05 ? C2 URI 502 B 1 HETATM 3 N N3 URI . . . G 4 17.355 -48.061 6.338 0.87 87.08 ? N3 URI 502 B 1 HETATM 4 C C4 URI . . . G 4 16.603 -47.954 5.182 0.87 85.7 ? C4 URI 502 B 1 HETATM 5 C C5 URI . . . G 4 17.277 -48.369 3.982 0.87 81.28 ? C5 URI 502 B 1 HETATM 6 C C6 URI . . . G 4 18.535 -48.822 4.025 0.87 83.67 ? C6 URI 502 B 1 HETATM 7 O O2 URI . . . G 4 19.234 -48.582 7.482 0.87 83.9 ? O2 URI 502 B 1 HETATM 8 O O4 URI . . . G 4 15.444 -47.521 5.261 0.87 85.07 ? O4 URI 502 B 1 HETATM 9 C C1' URI . . . G 4 20.608 -49.397 5.318 0.87 92.73 ? C1' URI 502 B 1 HETATM 10 C C2' URI . . . G 4 20.872 -50.767 4.715 0.87 88.01 ? C2' URI 502 B 1 HETATM 11 C C3' URI . . . G 4 22.394 -50.749 4.639 0.87 89.68 ? C3' URI 502 B 1 HETATM 12 C C4' URI . . . G 4 22.695 -49.286 4.291 0.87 90.44 ? C4' URI 502 B 1 HETATM 13 O O2' URI . . . G 4 20.359 -51.794 5.528 0.87 86.78 ? O2' URI 502 B 1 HETATM 14 O O3' URI . . . G 4 22.903 -51.035 5.941 0.87 84.94 ? O3' URI 502 B 1 HETATM 15 O O4' URI . . . G 4 21.5 -48.533 4.649 0.87 96.77 ? O4' URI 502 B 1 HETATM 16 C C5' URI . . . G 4 23.064 -49.015 2.857 0.87 91.19 ? C5' URI 502 B 1 HETATM 17 O O5' URI . . . G 4 24.444 -49.271 2.623 0.87 92.59 ? O5' URI 502 B 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 122 _model_server_stats.create_model_time_ms 94 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 17 #