data_6PF9 # _model_server_result.job_id wW1BHyVbIV_44Ga9djecdA _model_server_result.datetime_utc '2024-11-13 11:24:08' _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 6pf9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":602}' # _entry.id 6PF9 # _exptl.entry_id 6PF9 _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 94.87 _cell.angle_gamma 90 _cell.entry_id 6PF9 _cell.length_a 214.201 _cell.length_b 116.51 _cell.length_c 221.439 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PF9 _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,F,G,H,I,J 1 1,2 B,C,K,L,M,N,O,P,Q,R,S,T,EA,FA 2 1 D,U,V,W,X,Y,GA 3 1 E,Z,AA,BA,CA,DA,HA 3 3 # 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_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 3 'crystal symmetry operation' 3_555 x+1/2,y+1/2,z 1 0 0 0 1 0 0 0 1 107.1005 58.255 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 L N N ? 3 Q N N ? 3 V N N ? 3 AA 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 554 n n N1 C6 UFP sing 555 n n N1 C1' UFP sing 556 n n C2 N3 UFP sing 557 n n C2 O2 UFP doub 558 n n N3 C4 UFP sing 559 n n N3 HN3 UFP sing 560 n n C4 C5 UFP sing 561 n n C4 O4 UFP doub 562 n n C5 C6 UFP doub 563 n n C5 F5 UFP sing 564 n n C6 H6 UFP sing 565 n n C1' C2' UFP sing 566 n n C1' O4' UFP sing 567 n n C1' H1' UFP sing 568 n n C2' C3' UFP sing 569 n n C2' "H2'1" UFP sing 570 n n C2' "H2'2" UFP sing 571 n n C3' C4' UFP sing 572 n n C3' O3' UFP sing 573 n n C3' H3' UFP sing 574 n n C4' O4' UFP sing 575 n n C4' C5' UFP sing 576 n n C4' H4' UFP sing 577 n n O3' HO3' UFP sing 578 n n C5' O5' UFP sing 579 n n C5' "H5'1" UFP sing 580 n n C5' "H5'2" UFP sing 581 n n O5' P UFP sing 582 n n P O1P UFP doub 583 n n P O2P UFP sing 584 n n P O3P UFP sing 585 n n O2P HOP2 UFP sing 586 n n O3P HOP3 UFP sing 587 n n # _atom_sites.entry_id 6PF9 _atom_sites.fract_transf_matrix[1][1] 0.004669 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000398 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008583 _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] 0.004532 _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 OF7 A 1 603 603 OF7 M80 . I 5 MTX A 1 604 604 MTX MTX . J 6 SO4 A 1 605 5 SO4 SO4 . K 2 NDP B 1 601 601 NDP NDP . L 3 UFP B 1 602 602 UFP UFP . M 4 OF7 B 1 603 603 OF7 M80 . N 5 MTX B 1 604 604 MTX MTX . O 6 SO4 B 1 605 1 SO4 SO4 . P 2 NDP C 1 601 601 NDP NDP . Q 3 UFP C 1 602 602 UFP UFP . R 4 OF7 C 1 603 603 OF7 M80 . S 5 MTX C 1 604 604 MTX MTX . T 6 SO4 C 1 605 4 SO4 SO4 . U 2 NDP D 1 601 601 NDP NDP . V 3 UFP D 1 602 602 UFP UFP . W 4 OF7 D 1 603 603 OF7 M80 . X 5 MTX D 1 604 604 MTX MTX . Y 6 SO4 D 1 605 2 SO4 SO4 . Z 2 NDP E 1 601 601 NDP NDP . AA 3 UFP E 1 602 602 UFP UFP . BA 4 OF7 E 1 603 603 OF7 M80 . CA 5 MTX E 1 604 604 MTX MTX . DA 6 SO4 E 1 605 3 SO4 SO4 . EA 7 HOH B 1 701 3 HOH HOH . FA 7 HOH C 1 701 9 HOH HOH . FA 7 HOH C 2 702 7 HOH HOH . FA 7 HOH C 3 703 6 HOH HOH . FA 7 HOH C 4 704 12 HOH HOH . GA 7 HOH D 1 701 5 HOH HOH . GA 7 HOH D 2 702 10 HOH HOH . GA 7 HOH D 3 703 4 HOH HOH . GA 7 HOH D 4 704 1 HOH HOH . GA 7 HOH D 5 705 11 HOH HOH . HA 7 HOH E 1 701 8 HOH HOH . HA 7 HOH E 2 702 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 UFP . . . L 3 7.203 12.61 65.479 1 101.19 ? N1 UFP 602 B 1 HETATM 2 C C2 UFP . . . L 3 8.552 12.447 65.581 1 98.92 ? C2 UFP 602 B 1 HETATM 3 N N3 UFP . . . L 3 9.134 12.285 66.788 1 102.09 ? N3 UFP 602 B 1 HETATM 4 C C4 UFP . . . L 3 8.408 12.28 67.923 1 107.7 ? C4 UFP 602 B 1 HETATM 5 C C5 UFP . . . L 3 7.005 12.449 67.837 1 114.71 ? C5 UFP 602 B 1 HETATM 6 C C6 UFP . . . L 3 6.445 12.614 66.623 1 112.48 ? C6 UFP 602 B 1 HETATM 7 O O2 UFP . . . L 3 9.299 12.439 64.615 1 84.44 ? O2 UFP 602 B 1 HETATM 8 O O4 UFP . . . L 3 8.948 12.133 69.005 1 121.53 ? O4 UFP 602 B 1 HETATM 9 F F5 UFP . . . L 3 6.237 12.45 68.953 1 125.26 ? F5 UFP 602 B 1 HETATM 10 C C1' UFP . . . L 3 6.444 12.797 64.221 1 100.37 ? C1' UFP 602 B 1 HETATM 11 C C2' UFP . . . L 3 6.757 11.777 63.101 1 92.7 ? C2' UFP 602 B 1 HETATM 12 C C3' UFP . . . L 3 5.517 11.957 62.21 1 83.46 ? C3' UFP 602 B 1 HETATM 13 C C4' UFP . . . L 3 4.4 12.058 63.265 1 95.12 ? C4' UFP 602 B 1 HETATM 14 O O3' UFP . . . L 3 5.595 13.176 61.472 1 82.08 ? O3' UFP 602 B 1 HETATM 15 O O4' UFP . . . L 3 5.032 12.576 64.472 1 111.35 ? O4' UFP 602 B 1 HETATM 16 C C5' UFP . . . L 3 3.779 10.681 63.52 1 92.91 ? C5' UFP 602 B 1 HETATM 17 O O5' UFP . . . L 3 3.687 9.96 62.291 1 71.68 ? O5' UFP 602 B 1 HETATM 18 P P UFP . . . L 3 2.325 9.105 62.336 1 83.19 ? P UFP 602 B 1 HETATM 19 O O1P UFP . . . L 3 1.873 8.807 60.959 1 85.52 ? O1P UFP 602 B 1 HETATM 20 O O2P UFP . . . L 3 1.202 9.95 63.113 1 92.16 ? O2P UFP 602 B 1 HETATM 21 O O3P UFP . . . L 3 2.567 7.726 63.117 1 71.48 ? O3P UFP 602 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 40 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #