data_4YYY # _model_server_result.job_id VoLE-3qL-LLsDWWDtfaBAg _model_server_result.datetime_utc '2025-01-10 16:22:34' _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":"F","auth_seq_id":501}' # _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 . . . F 4 -1.06 -57.809 -17.779 0.9 88.08 ? N1 URI 501 B 1 HETATM 2 C C2 URI . . . F 4 -1.454 -59.117 -17.594 0.9 85.24 ? C2 URI 501 B 1 HETATM 3 N N3 URI . . . F 4 -2.751 -59.381 -17.979 0.9 82.88 ? N3 URI 501 B 1 HETATM 4 C C4 URI . . . F 4 -3.656 -58.488 -18.537 0.9 80.58 ? C4 URI 501 B 1 HETATM 5 C C5 URI . . . F 4 -3.164 -57.163 -18.708 0.9 87.17 ? C5 URI 501 B 1 HETATM 6 C C6 URI . . . F 4 -1.914 -56.886 -18.341 0.9 90.06 ? C6 URI 501 B 1 HETATM 7 O O2 URI . . . F 4 -0.721 -59.957 -17.1 0.9 86.8 ? O2 URI 501 B 1 HETATM 8 O O4 URI . . . F 4 -4.792 -58.842 -18.841 0.9 74.45 ? O4 URI 501 B 1 HETATM 9 C C1' URI . . . F 4 0.324 -57.446 -17.4 0.9 92.13 ? C1' URI 501 B 1 HETATM 10 C C2' URI . . . F 4 0.72 -56.076 -17.958 0.9 95.38 ? C2' URI 501 B 1 HETATM 11 C C3' URI . . . F 4 0.37 -55.163 -16.787 0.9 95.89 ? C3' URI 501 B 1 HETATM 12 C C4' URI . . . F 4 0.71 -56.019 -15.575 0.9 90.47 ? C4' URI 501 B 1 HETATM 13 O O2' URI . . . F 4 2.118 -56.067 -18.215 0.9 101.23 ? O2' URI 501 B 1 HETATM 14 O O3' URI . . . F 4 1.049 -53.925 -16.808 0.9 100.93 ? O3' URI 501 B 1 HETATM 15 O O4' URI . . . F 4 0.389 -57.37 -15.99 0.9 91.33 ? O4' URI 501 B 1 HETATM 16 C C5' URI . . . F 4 -0.049 -55.697 -14.314 0.9 87.76 ? C5' URI 501 B 1 HETATM 17 O O5' URI . . . F 4 -0.067 -56.805 -13.425 0.9 83.06 ? O5' URI 501 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 17 #