data_6PFD # _model_server_result.job_id RITrmijmCtUUb-D2mHclVA _model_server_result.datetime_utc '2024-12-01 06:55:40' _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 6pfd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":602}' # _entry.id 6PFD # _exptl.entry_id 6PFD _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 95.05 _cell.angle_gamma 90 _cell.entry_id 6PFD _cell.length_a 213.033 _cell.length_b 115.887 _cell.length_c 220.808 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PFD _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 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,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 1,2 # 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_858 -x+3,y,-z+3 -1 0 0 0 1 0 0 0 -1 580.789092 0 659.852643 # 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 548 n n N1 C6 UFP sing 549 n n N1 C1' UFP sing 550 n n C2 N3 UFP sing 551 n n C2 O2 UFP doub 552 n n N3 C4 UFP sing 553 n n N3 HN3 UFP sing 554 n n C4 C5 UFP sing 555 n n C4 O4 UFP doub 556 n n C5 C6 UFP doub 557 n n C5 F5 UFP sing 558 n n C6 H6 UFP sing 559 n n C1' C2' UFP sing 560 n n C1' O4' UFP sing 561 n n C1' H1' UFP sing 562 n n C2' C3' UFP sing 563 n n C2' "H2'1" UFP sing 564 n n C2' "H2'2" UFP sing 565 n n C3' C4' UFP sing 566 n n C3' O3' UFP sing 567 n n C3' H3' UFP sing 568 n n C4' O4' UFP sing 569 n n C4' C5' UFP sing 570 n n C4' H4' UFP sing 571 n n O3' HO3' UFP sing 572 n n C5' O5' UFP sing 573 n n C5' "H5'1" UFP sing 574 n n C5' "H5'2" UFP sing 575 n n O5' P UFP sing 576 n n P O1P UFP doub 577 n n P O2P UFP sing 578 n n P O3P UFP sing 579 n n O2P HOP2 UFP sing 580 n n O3P HOP3 UFP sing 581 n n # _atom_sites.entry_id 6PFD _atom_sites.fract_transf_matrix[1][1] 0.004694 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000414 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008629 _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] 0.004546 _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 1 601 601 NDP NDP . G 3 UFP A 1 602 602 UFP UFP . H 4 OEJ A 1 603 603 OEJ T11 . I 5 MTX A 1 604 604 MTX MTX . J 2 NDP B 1 601 601 NDP NDP . K 3 UFP B 1 602 602 UFP UFP . L 4 OEJ B 1 603 603 OEJ T11 . M 5 MTX B 1 604 604 MTX MTX . N 2 NDP C 1 601 601 NDP NDP . O 3 UFP C 1 602 602 UFP UFP . P 4 OEJ C 1 603 603 OEJ T11 . Q 5 MTX C 1 604 604 MTX MTX . R 2 NDP D 1 601 601 NDP NDP . S 3 UFP D 1 602 602 UFP UFP . T 4 OEJ D 1 603 603 OEJ T11 . U 5 MTX D 1 604 604 MTX MTX . V 2 NDP E 1 601 601 NDP NDP . W 3 UFP E 1 602 602 UFP UFP . X 4 OEJ E 1 603 603 OEJ T11 . Y 5 MTX E 1 604 604 MTX MTX . # 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 3 283.524 78.215 264.242 1 109.48 ? N1 UFP 602 D 1 HETATM 2 C C2 UFP . . . S 3 282.173 78.123 264.07 1 110.68 ? C2 UFP 602 D 1 HETATM 3 N N3 UFP . . . S 3 281.646 77.977 262.835 1 119.04 ? N3 UFP 602 D 1 HETATM 4 C C4 UFP . . . S 3 282.426 77.92 261.736 1 128.63 ? C4 UFP 602 D 1 HETATM 5 C C5 UFP . . . S 3 283.828 78.016 261.892 1 129.5 ? C5 UFP 602 D 1 HETATM 6 C C6 UFP . . . S 3 284.335 78.165 263.133 1 118.68 ? C6 UFP 602 D 1 HETATM 7 O O2 UFP . . . S 3 281.373 78.164 264.991 1 103.72 ? O2 UFP 602 D 1 HETATM 8 O O4 UFP . . . S 3 281.938 77.788 260.626 1 123.36 ? O4 UFP 602 D 1 HETATM 9 F F5 UFP . . . S 3 284.645 77.964 260.812 1 136.85 ? F5 UFP 602 D 1 HETATM 10 C C1' UFP . . . S 3 284.233 78.379 265.537 1 107.14 ? C1' UFP 602 D 1 HETATM 11 C C2' UFP . . . S 3 283.764 77.456 266.685 1 95.69 ? C2' UFP 602 D 1 HETATM 12 C C3' UFP . . . S 3 284.943 77.602 267.664 1 101.97 ? C3' UFP 602 D 1 HETATM 13 C C4' UFP . . . S 3 286.16 77.684 266.722 1 101.61 ? C4' UFP 602 D 1 HETATM 14 O O3' UFP . . . S 3 284.842 78.817 268.405 1 108.94 ? O3' UFP 602 D 1 HETATM 15 O O4' UFP . . . S 3 285.625 77.993 265.401 1 115.64 ? O4' UFP 602 D 1 HETATM 16 C C5' UFP . . . S 3 286.943 76.365 266.733 1 94.27 ? C5' UFP 602 D 1 HETATM 17 O O5' UFP . . . S 3 287.465 76.116 268.041 1 82.93 ? O5' UFP 602 D 1 HETATM 18 P P UFP . . . S 3 288.375 74.785 267.993 1 79.89 ? P UFP 602 D 1 HETATM 19 O O1P UFP . . . S 3 289.33 74.824 266.702 1 88.44 ? O1P UFP 602 D 1 HETATM 20 O O2P UFP . . . S 3 289.209 74.706 269.212 1 102.73 ? O2P UFP 602 D 1 HETATM 21 O O3P UFP . . . S 3 287.436 73.485 267.919 1 77.24 ? O3P UFP 602 D 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 236 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #