data_6PF6 # _model_server_result.job_id LBLfzrhUkcRwktLqYxW-dg _model_server_result.datetime_utc '2024-11-13 11:45:08' _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 6pf6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":600}' # _entry.id 6PF6 # _exptl.entry_id 6PF6 _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 4 _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 6PF6 _cell.length_a 152.215 _cell.length_b 152.215 _cell.length_c 107.07 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PF6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,K,L 1 1 C,H,I,M 2 1 D,J,N 2 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' 6_555 x+1/2,-y+1/2,-z+3/4 1 0 0 0 -1 0 0 0 -1 76.1075 76.1075 80.3025 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 G N N ? 2 H N N ? 2 J 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 411 n n N1 C6 UMP sing 412 n n N1 C1' UMP sing 413 n n C2 N3 UMP sing 414 n n C2 O2 UMP doub 415 n n N3 C4 UMP sing 416 n n N3 HN3 UMP sing 417 n n C4 C5 UMP sing 418 n n C4 O4 UMP doub 419 n n C5 C6 UMP doub 420 n n C5 H5 UMP sing 421 n n C6 H6 UMP sing 422 n n C1' C2' UMP sing 423 n n C1' O4' UMP sing 424 n n C1' H1' UMP sing 425 n n C2' C3' UMP sing 426 n n C2' H2' UMP sing 427 n n C2' "H2''" UMP sing 428 n n C3' C4' UMP sing 429 n n C3' O3' UMP sing 430 n n C3' H3' UMP sing 431 n n C4' O4' UMP sing 432 n n C4' C5' UMP sing 433 n n C4' H4' UMP sing 434 n n O3' HO3' UMP sing 435 n n C5' O5' UMP sing 436 n n C5' H5' UMP sing 437 n n C5' "H5''" UMP sing 438 n n O5' P UMP sing 439 n n P OP1 UMP doub 440 n n P OP2 UMP sing 441 n n P OP3 UMP sing 442 n n OP2 HOP2 UMP sing 443 n n OP3 HOP3 UMP sing 444 n n # _atom_sites.entry_id 6PF6 _atom_sites.fract_transf_matrix[1][1] 0.00657 _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] 0.00657 _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] 0.00934 _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 E 2 UMP B 1 600 600 UMP UMP . F 3 OEJ B 1 601 601 OEJ T11 . G 2 UMP A 1 600 600 UMP UMP . H 2 UMP C 1 600 600 UMP UMP . I 3 OEJ C 1 601 601 OEJ T11 . J 2 UMP D 1 600 600 UMP UMP . K 4 HOH B 1 701 28 HOH HOH . K 4 HOH B 2 702 1 HOH HOH . K 4 HOH B 3 703 6 HOH HOH . K 4 HOH B 4 704 11 HOH HOH . K 4 HOH B 5 705 4 HOH HOH . K 4 HOH B 6 706 18 HOH HOH . L 4 HOH A 1 701 9 HOH HOH . L 4 HOH A 2 702 10 HOH HOH . L 4 HOH A 3 703 8 HOH HOH . L 4 HOH A 4 704 7 HOH HOH . L 4 HOH A 5 705 26 HOH HOH . M 4 HOH C 1 701 15 HOH HOH . M 4 HOH C 2 702 25 HOH HOH . M 4 HOH C 3 703 3 HOH HOH . M 4 HOH C 4 704 20 HOH HOH . M 4 HOH C 5 705 16 HOH HOH . M 4 HOH C 6 706 30 HOH HOH . N 4 HOH D 1 701 13 HOH HOH . N 4 HOH D 2 702 24 HOH HOH . N 4 HOH D 3 703 29 HOH HOH . N 4 HOH D 4 704 22 HOH HOH . N 4 HOH D 5 705 23 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 . . . G 2 37.933 -14.279 12.945 1 67.39 ? N1 UMP 600 A 1 HETATM 2 C C2 UMP . . . G 2 37.247 -13.53 11.959 1 66.17 ? C2 UMP 600 A 1 HETATM 3 N N3 UMP . . . G 2 36.064 -12.903 12.347 1 66.53 ? N3 UMP 600 A 1 HETATM 4 C C4 UMP . . . G 2 35.499 -12.95 13.623 1 71.93 ? C4 UMP 600 A 1 HETATM 5 C C5 UMP . . . G 2 36.254 -13.737 14.592 1 68.16 ? C5 UMP 600 A 1 HETATM 6 C C6 UMP . . . G 2 37.402 -14.354 14.226 1 68.1 ? C6 UMP 600 A 1 HETATM 7 O O2 UMP . . . G 2 37.639 -13.409 10.8 1 67.36 ? O2 UMP 600 A 1 HETATM 8 O O4 UMP . . . G 2 34.447 -12.356 13.854 1 69.5 ? O4 UMP 600 A 1 HETATM 9 C C1' UMP . . . G 2 39.226 -14.997 12.626 1 66.08 ? C1' UMP 600 A 1 HETATM 10 C C2' UMP . . . G 2 40.387 -14.061 12.271 1 65.71 ? C2' UMP 600 A 1 HETATM 11 C C3' UMP . . . G 2 41.564 -14.918 12.701 1 67.33 ? C3' UMP 600 A 1 HETATM 12 C C4' UMP . . . G 2 41.032 -15.632 13.949 1 68.93 ? C4' UMP 600 A 1 HETATM 13 O O3' UMP . . . G 2 41.922 -15.825 11.678 1 68.29 ? O3' UMP 600 A 1 HETATM 14 O O4' UMP . . . G 2 39.618 -15.706 13.759 1 72.13 ? O4' UMP 600 A 1 HETATM 15 C C5' UMP . . . G 2 41.355 -14.885 15.254 1 61.34 ? C5' UMP 600 A 1 HETATM 16 O O5' UMP . . . G 2 42.717 -15.008 15.632 1 61.27 ? O5' UMP 600 A 1 HETATM 17 P P UMP . . . G 2 43.561 -13.778 16.274 1 64.86 ? P UMP 600 A 1 HETATM 18 O OP1 UMP . . . G 2 43.601 -12.712 15.056 1 62.85 -1 OP1 UMP 600 A 1 HETATM 19 O OP2 UMP . . . G 2 43.074 -13.271 17.588 1 68.76 ? OP2 UMP 600 A 1 HETATM 20 O OP3 UMP . . . G 2 45.078 -14.353 16.274 1 67.65 -1 OP3 UMP 600 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #