data_5X5Q # _model_server_result.job_id tybQqgiFA7_Xcm_OOJ_ekg _model_server_result.datetime_utc '2024-11-16 19:53:55' _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 5x5q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":401}' # _entry.id 5X5Q # _exptl.entry_id 5X5Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 6 _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 5X5Q _cell.length_a 107.835 _cell.length_b 107.835 _cell.length_c 314.951 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5X5Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,G,H,M,N,S,V 1 1 B,E,I,J,O,P,T 2 1 C,F,K,L,Q,R,U,W 3 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 G N N ? 2 I N N ? 2 K N N ? 2 M N N ? 2 O N N ? 2 Q N N # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 UMP sing 414 n n N1 C6 UMP sing 415 n n N1 C1' UMP sing 416 n n C2 N3 UMP sing 417 n n C2 O2 UMP doub 418 n n N3 C4 UMP sing 419 n n N3 HN3 UMP sing 420 n n C4 C5 UMP sing 421 n n C4 O4 UMP doub 422 n n C5 C6 UMP doub 423 n n C5 H5 UMP sing 424 n n C6 H6 UMP sing 425 n n C1' C2' UMP sing 426 n n C1' O4' UMP sing 427 n n C1' H1' UMP sing 428 n n C2' C3' UMP sing 429 n n C2' H2' UMP sing 430 n n C2' "H2''" UMP sing 431 n n C3' C4' UMP sing 432 n n C3' O3' UMP sing 433 n n C3' H3' UMP sing 434 n n C4' O4' UMP sing 435 n n C4' C5' UMP sing 436 n n C4' H4' UMP sing 437 n n O3' HO3' UMP sing 438 n n C5' O5' UMP sing 439 n n C5' H5' UMP sing 440 n n C5' "H5''" UMP sing 441 n n O5' P UMP sing 442 n n P OP1 UMP doub 443 n n P OP2 UMP sing 444 n n P OP3 UMP sing 445 n n OP2 HOP2 UMP sing 446 n n OP3 HOP3 UMP sing 447 n n # _atom_sites.entry_id 5X5Q _atom_sites.fract_transf_matrix[1][1] 0.009273 _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] 0.009273 _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] 0.003175 _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 G 2 UMP A 1 401 1 UMP UMP . H 3 D16 A 1 402 1 D16 RTX . I 2 UMP B 1 401 2 UMP UMP . J 3 D16 B 1 402 2 D16 RTX . K 2 UMP C 1 401 3 UMP UMP . L 3 D16 C 1 402 3 D16 RTX . M 2 UMP D 1 401 4 UMP UMP . N 3 D16 D 1 402 4 D16 RTX . O 2 UMP E 1 401 5 UMP UMP . P 3 D16 E 1 402 5 D16 RTX . Q 2 UMP F 1 401 6 UMP UMP . R 3 D16 F 1 402 6 D16 RTX . S 4 HOH A 1 501 1 HOH HOH . S 4 HOH A 2 502 9 HOH HOH . T 4 HOH B 1 501 5 HOH HOH . T 4 HOH B 2 502 8 HOH HOH . T 4 HOH B 3 503 2 HOH HOH . T 4 HOH B 4 504 4 HOH HOH . U 4 HOH C 1 501 3 HOH HOH . V 4 HOH D 1 501 7 HOH HOH . V 4 HOH D 2 502 10 HOH HOH . W 4 HOH F 1 501 6 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 UMP . . . I 2 68.618 36.94 1.27 1 35.36 ? N1 UMP 401 B 1 HETATM 2 C C2 UMP . . . I 2 69.492 37.338 0.163 1 34.19 ? C2 UMP 401 B 1 HETATM 3 N N3 UMP . . . I 2 70.681 38.101 0.535 1 32.55 ? N3 UMP 401 B 1 HETATM 4 C C4 UMP . . . I 2 71.034 38.462 1.857 1 34.21 ? C4 UMP 401 B 1 HETATM 5 C C5 UMP . . . I 2 70.125 38.049 2.923 1 35.52 ? C5 UMP 401 B 1 HETATM 6 C C6 UMP . . . I 2 68.923 37.268 2.625 1 35.23 ? C6 UMP 401 B 1 HETATM 7 O O2 UMP . . . I 2 69.251 37.065 -1.023 1 33.1 ? O2 UMP 401 B 1 HETATM 8 O O4 UMP . . . I 2 72.047 39.125 2.105 1 37.82 ? O4 UMP 401 B 1 HETATM 9 C C1' UMP . . . I 2 67.422 36.153 1 1 36.93 ? C1' UMP 401 B 1 HETATM 10 C C2' UMP . . . I 2 67.267 34.802 0.369 1 37.87 ? C2' UMP 401 B 1 HETATM 11 C C3' UMP . . . I 2 65.926 34.38 0.644 1 37.43 ? C3' UMP 401 B 1 HETATM 12 C C4' UMP . . . I 2 65.602 35.14 1.873 1 37.94 ? C4' UMP 401 B 1 HETATM 13 O O3' UMP . . . I 2 65.114 34.75 -0.422 1 37.82 ? O3' UMP 401 B 1 HETATM 14 O O4' UMP . . . I 2 66.33 36.369 1.845 1 34.6 ? O4' UMP 401 B 1 HETATM 15 C C5' UMP . . . I 2 66.017 34.331 3.064 1 38.73 ? C5' UMP 401 B 1 HETATM 16 O O5' UMP . . . I 2 65.265 33.216 3.327 1 38.76 ? O5' UMP 401 B 1 HETATM 17 P P UMP . . . I 2 65.726 31.922 4.037 1 35.81 ? P UMP 401 B 1 HETATM 18 O OP1 UMP . . . I 2 66.609 31.264 2.992 1 39.01 -1 OP1 UMP 401 B 1 HETATM 19 O OP2 UMP . . . I 2 64.462 31.111 4.327 1 33.7 ? OP2 UMP 401 B 1 HETATM 20 O OP3 UMP . . . I 2 66.503 32.225 5.272 1 36.56 -1 OP3 UMP 401 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #