data_7CCA # _model_server_result.job_id p0uSB9oT2NDSoYghmL5IuQ _model_server_result.datetime_utc '2024-11-28 14:58:46' _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 7cca # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 7CCA # _exptl.entry_id 7CCA _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 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 7CCA _cell.length_a 92.385 _cell.length_b 92.385 _cell.length_c 234.72 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7CCA _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E 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 415 n n N1 C6 UMP sing 416 n n N1 C1' UMP sing 417 n n C2 N3 UMP sing 418 n n C2 O2 UMP doub 419 n n N3 C4 UMP sing 420 n n N3 HN3 UMP sing 421 n n C4 C5 UMP sing 422 n n C4 O4 UMP doub 423 n n C5 C6 UMP doub 424 n n C5 H5 UMP sing 425 n n C6 H6 UMP sing 426 n n C1' C2' UMP sing 427 n n C1' O4' UMP sing 428 n n C1' H1' UMP sing 429 n n C2' C3' UMP sing 430 n n C2' H2' UMP sing 431 n n C2' "H2''" UMP sing 432 n n C3' C4' UMP sing 433 n n C3' O3' UMP sing 434 n n C3' H3' UMP sing 435 n n C4' O4' UMP sing 436 n n C4' C5' UMP sing 437 n n C4' H4' UMP sing 438 n n O3' HO3' UMP sing 439 n n C5' O5' UMP sing 440 n n C5' H5' UMP sing 441 n n C5' "H5''" UMP sing 442 n n O5' P UMP sing 443 n n P OP1 UMP doub 444 n n P OP2 UMP sing 445 n n P OP3 UMP sing 446 n n OP2 HOP2 UMP sing 447 n n OP3 HOP3 UMP sing 448 n n # _atom_sites.entry_id 7CCA _atom_sites.fract_transf_matrix[1][1] 0.010824 _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] 0.010824 _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] 0.00426 _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 UMP A 1 301 1 UMP UMP . D 3 MTX A 1 302 1 MTX MTX . E 2 UMP B 1 301 2 UMP UMP . F 3 MTX B 1 302 2 MTX MTX . G 4 HOH A 1 401 10 HOH HOH . G 4 HOH A 2 402 1 HOH HOH . G 4 HOH A 3 403 24 HOH HOH . G 4 HOH A 4 404 26 HOH HOH . G 4 HOH A 5 405 17 HOH HOH . G 4 HOH A 6 406 20 HOH HOH . G 4 HOH A 7 407 2 HOH HOH . G 4 HOH A 8 408 7 HOH HOH . G 4 HOH A 9 409 16 HOH HOH . G 4 HOH A 10 410 19 HOH HOH . G 4 HOH A 11 411 14 HOH HOH . G 4 HOH A 12 412 28 HOH HOH . G 4 HOH A 13 413 31 HOH HOH . H 4 HOH B 1 401 4 HOH HOH . H 4 HOH B 2 402 18 HOH HOH . H 4 HOH B 3 403 21 HOH HOH . H 4 HOH B 4 404 22 HOH HOH . H 4 HOH B 5 405 11 HOH HOH . H 4 HOH B 6 406 29 HOH HOH . H 4 HOH B 7 407 15 HOH HOH . H 4 HOH B 8 408 9 HOH HOH . H 4 HOH B 9 409 5 HOH HOH . H 4 HOH B 10 410 6 HOH HOH . H 4 HOH B 11 411 8 HOH HOH . H 4 HOH B 12 412 25 HOH HOH . H 4 HOH B 13 413 23 HOH HOH . H 4 HOH B 14 414 12 HOH HOH . H 4 HOH B 15 415 27 HOH HOH . H 4 HOH B 16 416 13 HOH HOH . H 4 HOH B 17 417 3 HOH HOH . H 4 HOH B 18 418 30 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 . . . E 2 19.269 -32.161 -27.436 1 57.01 ? N1 UMP 301 B 1 HETATM 2 C C2 UMP . . . E 2 18.901 -30.828 -27.592 1 55.97 ? C2 UMP 301 B 1 HETATM 3 N N3 UMP . . . E 2 17.612 -30.626 -28.028 1 59.84 ? N3 UMP 301 B 1 HETATM 4 C C4 UMP . . . E 2 16.674 -31.593 -28.353 1 66.43 ? C4 UMP 301 B 1 HETATM 5 C C5 UMP . . . E 2 17.133 -32.944 -28.187 1 64.5 ? C5 UMP 301 B 1 HETATM 6 C C6 UMP . . . E 2 18.387 -33.175 -27.755 1 60.07 ? C6 UMP 301 B 1 HETATM 7 O O2 UMP . . . E 2 19.647 -29.885 -27.349 1 47.44 ? O2 UMP 301 B 1 HETATM 8 O O4 UMP . . . E 2 15.554 -31.251 -28.741 1 72.52 ? O4 UMP 301 B 1 HETATM 9 C C1' UMP . . . E 2 20.673 -32.474 -27.016 1 57.36 ? C1' UMP 301 B 1 HETATM 10 C C2' UMP . . . E 2 21.019 -32.281 -25.545 1 60.41 ? C2' UMP 301 B 1 HETATM 11 C C3' UMP . . . E 2 22.218 -33.212 -25.402 1 57.95 ? C3' UMP 301 B 1 HETATM 12 C C4' UMP . . . E 2 21.761 -34.403 -26.235 1 54.41 ? C4' UMP 301 B 1 HETATM 13 O O3' UMP . . . E 2 23.419 -32.659 -25.927 1 48.67 ? O3' UMP 301 B 1 HETATM 14 O O4' UMP . . . E 2 20.92 -33.851 -27.269 1 56.92 ? O4' UMP 301 B 1 HETATM 15 C C5' UMP . . . E 2 20.973 -35.432 -25.467 1 56.86 ? C5' UMP 301 B 1 HETATM 16 O O5' UMP . . . E 2 21.89 -36.188 -24.661 1 58.94 ? O5' UMP 301 B 1 HETATM 17 P P UMP . . . E 2 21.607 -36.443 -23.093 1 56.19 ? P UMP 301 B 1 HETATM 18 O OP1 UMP . . . E 2 22.935 -36.986 -22.554 1 56.14 ? OP1 UMP 301 B 1 HETATM 19 O OP2 UMP . . . E 2 20.467 -37.45 -23.016 1 53.29 ? OP2 UMP 301 B 1 HETATM 20 O OP3 UMP . . . E 2 21.268 -35.103 -22.492 1 55.26 ? OP3 UMP 301 B 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 344 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #