data_4KY8 # _model_server_result.job_id -SqpEQY7jwcTPSzDA0NzRQ _model_server_result.datetime_utc '2024-11-04 22:56:23' _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 4ky8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":602}' # _entry.id 4KY8 # _exptl.entry_id 4KY8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 326.172 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 5 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 94.36 _cell.angle_gamma 90 _cell.entry_id 4KY8 _cell.length_a 214.162 _cell.length_b 115.665 _cell.length_c 218.767 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KY8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 monomeric 1 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,B,F,G,H,I,J,K,L,M 1 1 C,D,N,O,P,Q,R,S,T,U 2 1 E,V,W,X,Y 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 ? 3 G N N ? 3 K N N ? 3 O N N ? 3 S N N ? 3 W N N # _chem_comp.formula 'C9 H12 F N2 O8 P' _chem_comp.formula_weight 326.172 _chem_comp.id UFP _chem_comp.mon_nstd_flag . _chem_comp.name "5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _chem_comp.type 'dna linking' _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 UFP sing 547 n n N1 C6 UFP sing 548 n n N1 C1' UFP sing 549 n n C2 N3 UFP sing 550 n n C2 O2 UFP doub 551 n n N3 C4 UFP sing 552 n n N3 HN3 UFP sing 553 n n C4 C5 UFP sing 554 n n C4 O4 UFP doub 555 n n C5 C6 UFP doub 556 n n C5 F5 UFP sing 557 n n C6 H6 UFP sing 558 n n C1' C2' UFP sing 559 n n C1' O4' UFP sing 560 n n C1' H1' UFP sing 561 n n C2' C3' UFP sing 562 n n C2' "H2'1" UFP sing 563 n n C2' "H2'2" UFP sing 564 n n C3' C4' UFP sing 565 n n C3' O3' UFP sing 566 n n C3' H3' UFP sing 567 n n C4' O4' UFP sing 568 n n C4' C5' UFP sing 569 n n C4' H4' UFP sing 570 n n O3' HO3' UFP sing 571 n n C5' O5' UFP sing 572 n n C5' "H5'1" UFP sing 573 n n C5' "H5'2" UFP sing 574 n n O5' P UFP sing 575 n n P O1P UFP doub 576 n n P O2P UFP sing 577 n n P O3P UFP sing 578 n n O2P HOP2 UFP sing 579 n n O3P HOP3 UFP sing 580 n n # _atom_sites.entry_id 4KY8 _atom_sites.fract_transf_matrix[1][1] 0.004669 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000356 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008646 _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] 0.004584 _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 F 2 NDP A 1 601 207 NDP NDP . G 3 UFP A 1 602 1 UFP UFP . H 4 MTX A 1 603 161 MTX MTX . I 5 1UF A 1 604 1 1UF 1UF . J 2 NDP B 1 601 207 NDP NDP . K 3 UFP B 1 602 1 UFP UFP . L 4 MTX B 1 603 161 MTX MTX . M 5 1UF B 1 604 1 1UF 1UF . N 2 NDP C 1 601 207 NDP NDP . O 3 UFP C 1 602 1 UFP UFP . P 4 MTX C 1 603 161 MTX MTX . Q 5 1UF C 1 604 1 1UF 1UF . R 2 NDP D 1 601 207 NDP NDP . S 3 UFP D 1 602 1 UFP UFP . T 4 MTX D 1 603 161 MTX MTX . U 5 1UF D 1 604 1 1UF 1UF . V 2 NDP E 1 601 207 NDP NDP . W 3 UFP E 1 602 1 UFP UFP . X 4 MTX E 1 603 161 MTX MTX . Y 5 1UF E 1 604 1 1UF 1UF . # 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 UFP . . . S 3 189.276 -119.226 501.325 1 95.27 ? N1 UFP 602 D 1 HETATM 2 C C2 UFP . . . S 3 190.625 -119.235 501.176 1 97.49 ? C2 UFP 602 D 1 HETATM 3 N N3 UFP . . . S 3 191.434 -119.404 502.239 1 99.35 ? N3 UFP 602 D 1 HETATM 4 C C4 UFP . . . S 3 190.926 -119.566 503.476 1 102.13 ? C4 UFP 602 D 1 HETATM 5 C C5 UFP . . . S 3 189.523 -119.557 503.651 1 103.34 ? C5 UFP 602 D 1 HETATM 6 C C6 UFP . . . S 3 188.73 -119.383 502.574 1 95.66 ? C6 UFP 602 D 1 HETATM 7 O O2 UFP . . . S 3 191.156 -119.093 500.089 1 96.52 ? O2 UFP 602 D 1 HETATM 8 O O4 UFP . . . S 3 191.663 -119.719 504.433 1 99.04 ? O4 UFP 602 D 1 HETATM 9 F F5 UFP . . . S 3 188.987 -119.718 504.882 1 120.41 ? F5 UFP 602 D 1 HETATM 10 C C1' UFP . . . S 3 188.336 -119.042 500.201 1 95.68 ? C1' UFP 602 D 1 HETATM 11 C C2' UFP . . . S 3 188.459 -120.148 499.131 1 94.5 ? C2' UFP 602 D 1 HETATM 12 C C3' UFP . . . S 3 187.112 -120.022 498.394 1 93.13 ? C3' UFP 602 D 1 HETATM 13 C C4' UFP . . . S 3 186.166 -119.39 499.439 1 92.6 ? C4' UFP 602 D 1 HETATM 14 O O3' UFP . . . S 3 187.239 -119.152 497.27 1 89.04 ? O3' UFP 602 D 1 HETATM 15 O O4' UFP . . . S 3 186.96 -119.162 500.634 1 94.28 ? O4' UFP 602 D 1 HETATM 16 C C5' UFP . . . S 3 184.983 -120.32 499.729 1 91.07 ? C5' UFP 602 D 1 HETATM 17 O O5' UFP . . . S 3 185.413 -121.683 499.778 1 95.62 ? O5' UFP 602 D 1 HETATM 18 P P UFP . . . S 3 184.518 -122.515 498.727 1 90.93 ? P UFP 602 D 1 HETATM 19 O O1P UFP . . . S 3 185.33 -122.854 497.539 1 84.95 ? O1P UFP 602 D 1 HETATM 20 O O2P UFP . . . S 3 183.259 -121.623 498.272 1 86.35 -1 O2P UFP 602 D 1 HETATM 21 O O3P UFP . . . S 3 183.992 -123.871 499.415 1 90.92 -1 O3P UFP 602 D 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 21 #