data_6PF4 # _model_server_result.job_id a1HeyVOLQpVaQ3eSkbbwHw _model_server_result.datetime_utc '2024-11-22 22:00:16' _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 6pf4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":600}' # _entry.id 6PF4 # _exptl.entry_id 6PF4 _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 6PF4 _cell.length_a 92.19 _cell.length_b 96.437 _cell.length_c 135.719 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PF4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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,D,E,F,K,L,M,P 1 1 B,G,H,N 2 1 C,I,J,O 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' 2_544 -x+1/2,-y-1,z-1/2 -1 0 0 0 -1 0 0 0 1 46.095 -96.437 -67.8595 # 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 I N N ? 2 K 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 6PF4 _atom_sites.fract_transf_matrix[1][1] 0.010847 _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] 0.010369 _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] 0.007368 _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 OF7 B 1 601 601 OF7 TS5 . G 2 UMP A 1 600 600 UMP UMP . H 3 OF7 A 1 601 601 OF7 TS5 . I 2 UMP C 1 600 600 UMP UMP . J 3 OF7 C 1 601 601 OF7 TS5 . K 2 UMP D 1 600 600 UMP UMP . L 3 OF7 D 1 601 601 OF7 TS5 . M 4 HOH B 1 701 16 HOH HOH . M 4 HOH B 2 702 5 HOH HOH . M 4 HOH B 3 703 18 HOH HOH . M 4 HOH B 4 704 7 HOH HOH . M 4 HOH B 5 705 21 HOH HOH . M 4 HOH B 6 706 1 HOH HOH . N 4 HOH A 1 701 11 HOH HOH . N 4 HOH A 2 702 27 HOH HOH . N 4 HOH A 3 703 26 HOH HOH . N 4 HOH A 4 704 15 HOH HOH . N 4 HOH A 5 705 28 HOH HOH . N 4 HOH A 6 706 23 HOH HOH . N 4 HOH A 7 707 8 HOH HOH . N 4 HOH A 8 708 4 HOH HOH . N 4 HOH A 9 709 22 HOH HOH . N 4 HOH A 10 710 14 HOH HOH . O 4 HOH C 1 701 25 HOH HOH . O 4 HOH C 2 702 29 HOH HOH . O 4 HOH C 3 703 17 HOH HOH . O 4 HOH C 4 704 6 HOH HOH . O 4 HOH C 5 705 3 HOH HOH . O 4 HOH C 6 706 13 HOH HOH . P 4 HOH D 1 701 10 HOH HOH . P 4 HOH D 2 702 9 HOH HOH . P 4 HOH D 3 703 12 HOH HOH . P 4 HOH D 4 704 2 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 29.629 -38.358 25.139 1 31.04 ? N1 UMP 600 C 1 HETATM 2 C C2 UMP . . . I 2 29.299 -37.539 26.235 1 30.04 ? C2 UMP 600 C 1 HETATM 3 N N3 UMP . . . I 2 27.958 -37.18 26.374 1 28.55 ? N3 UMP 600 C 1 HETATM 4 C C4 UMP . . . I 2 26.918 -37.558 25.522 1 29.3 ? C4 UMP 600 C 1 HETATM 5 C C5 UMP . . . I 2 27.331 -38.399 24.411 1 29.95 ? C5 UMP 600 C 1 HETATM 6 C C6 UMP . . . I 2 28.632 -38.741 24.257 1 29.66 ? C6 UMP 600 C 1 HETATM 7 O O2 UMP . . . I 2 30.135 -37.149 27.044 1 28.59 ? O2 UMP 600 C 1 HETATM 8 O O4 UMP . . . I 2 25.763 -37.19 25.728 1 28.68 ? O4 UMP 600 C 1 HETATM 9 C C1' UMP . . . I 2 31.051 -38.801 24.902 1 29.44 ? C1' UMP 600 C 1 HETATM 10 C C2' UMP . . . I 2 31.599 -39.728 25.989 1 29.54 ? C2' UMP 600 C 1 HETATM 11 C C3' UMP . . . I 2 32.647 -40.483 25.193 1 30.21 ? C3' UMP 600 C 1 HETATM 12 C C4' UMP . . . I 2 32.003 -40.608 23.807 1 31.12 ? C4' UMP 600 C 1 HETATM 13 O O3' UMP . . . I 2 33.857 -39.755 25.158 1 29.97 ? O3' UMP 600 C 1 HETATM 14 O O4' UMP . . . I 2 31.052 -39.548 23.732 1 29.71 ? O4' UMP 600 C 1 HETATM 15 C C5' UMP . . . I 2 31.29 -41.95 23.59 1 30.45 ? C5' UMP 600 C 1 HETATM 16 O O5' UMP . . . I 2 32.214 -43.002 23.392 1 30.06 ? O5' UMP 600 C 1 HETATM 17 P P UMP . . . I 2 32.037 -44.452 24.094 1 29.8 ? P UMP 600 C 1 HETATM 18 O OP1 UMP . . . I 2 33.317 -45.257 23.504 1 30.22 -1 OP1 UMP 600 C 1 HETATM 19 O OP2 UMP . . . I 2 30.707 -45.094 23.909 1 29.8 ? OP2 UMP 600 C 1 HETATM 20 O OP3 UMP . . . I 2 32.46 -44.166 25.634 1 30.1 -1 OP3 UMP 600 C 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #