data_6PFB # _model_server_result.job_id m7kalssATKSYSVKhUkXXmw _model_server_result.datetime_utc '2024-11-25 08:37:53' _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 6pfb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":602}' # _entry.id 6PFB # _exptl.entry_id 6PFB _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 94.75 _cell.angle_gamma 90 _cell.entry_id 6PFB _cell.length_a 213.994 _cell.length_b 116.238 _cell.length_c 221.672 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PFB _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_658 -x+1,y,-z+3 -1 0 0 0 1 0 0 0 -1 158.925217 0 662.732004 # 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 551 n n N1 C6 UFP sing 552 n n N1 C1' UFP sing 553 n n C2 N3 UFP sing 554 n n C2 O2 UFP doub 555 n n N3 C4 UFP sing 556 n n N3 HN3 UFP sing 557 n n C4 C5 UFP sing 558 n n C4 O4 UFP doub 559 n n C5 C6 UFP doub 560 n n C5 F5 UFP sing 561 n n C6 H6 UFP sing 562 n n C1' C2' UFP sing 563 n n C1' O4' UFP sing 564 n n C1' H1' UFP sing 565 n n C2' C3' UFP sing 566 n n C2' "H2'1" UFP sing 567 n n C2' "H2'2" UFP sing 568 n n C3' C4' UFP sing 569 n n C3' O3' UFP sing 570 n n C3' H3' UFP sing 571 n n C4' O4' UFP sing 572 n n C4' C5' UFP sing 573 n n C4' H4' UFP sing 574 n n O3' HO3' UFP sing 575 n n C5' O5' UFP sing 576 n n C5' "H5'1" UFP sing 577 n n C5' "H5'2" UFP sing 578 n n O5' P UFP sing 579 n n P O1P UFP doub 580 n n P O2P UFP sing 581 n n P O3P UFP sing 582 n n O2P HOP2 UFP sing 583 n n O3P HOP3 UFP sing 584 n n # _atom_sites.entry_id 6PFB _atom_sites.fract_transf_matrix[1][1] 0.004673 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000389 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008603 _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] 0.004527 _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 OG4 A 1 603 603 OG4 TS7 . 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 OG4 B 1 603 603 OG4 TS7 . 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 OG4 C 1 603 603 OG4 TS7 . 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 OG4 D 1 603 603 OG4 TS7 . 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 OG4 E 1 603 603 OG4 TS7 . 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 . . . O 3 72.182 79.519 265.659 1 108.49 ? N1 UFP 602 C 1 HETATM 2 C C2 UFP . . . O 3 70.854 79.202 265.595 1 111.31 ? C2 UFP 602 C 1 HETATM 3 N N3 UFP . . . O 3 70.245 79.047 264.402 1 113.1 ? N3 UFP 602 C 1 HETATM 4 C C4 UFP . . . O 3 70.913 79.2 263.243 1 112.76 ? C4 UFP 602 C 1 HETATM 5 C C5 UFP . . . O 3 72.287 79.532 263.287 1 115.03 ? C5 UFP 602 C 1 HETATM 6 C C6 UFP . . . O 3 72.878 79.686 264.487 1 110.43 ? C6 UFP 602 C 1 HETATM 7 O O2 UFP . . . O 3 70.144 79.039 266.574 1 103.75 ? O2 UFP 602 C 1 HETATM 8 O O4 UFP . . . O 3 70.346 79.057 262.175 1 115.28 ? O4 UFP 602 C 1 HETATM 9 F F5 UFP . . . O 3 72.995 79.695 262.144 1 125.09 ? F5 UFP 602 C 1 HETATM 10 C C1' UFP . . . O 3 72.991 79.725 266.886 1 110.04 ? C1' UFP 602 C 1 HETATM 11 C C2' UFP . . . O 3 72.715 78.773 268.074 1 105.23 ? C2' UFP 602 C 1 HETATM 12 C C3' UFP . . . O 3 73.981 79.023 268.908 1 101.5 ? C3' UFP 602 C 1 HETATM 13 C C4' UFP . . . O 3 75.062 79.026 267.812 1 112.71 ? C4' UFP 602 C 1 HETATM 14 O O3' UFP . . . O 3 73.93 80.306 269.533 1 105.81 ? O3' UFP 602 C 1 HETATM 15 O O4' UFP . . . O 3 74.389 79.458 266.593 1 119.89 ? O4' UFP 602 C 1 HETATM 16 C C5' UFP . . . O 3 75.663 77.626 267.65 1 106.45 ? C5' UFP 602 C 1 HETATM 17 O O5' UFP . . . O 3 76.879 77.544 268.395 1 101.07 ? O5' UFP 602 C 1 HETATM 18 P P UFP . . . O 3 77.022 76.05 268.98 1 101.74 ? P UFP 602 C 1 HETATM 19 O O1P UFP . . . O 3 77.882 75.147 267.965 1 69.38 ? O1P UFP 602 C 1 HETATM 20 O O2P UFP . . . O 3 77.773 76.11 270.399 1 95.33 ? O2P UFP 602 C 1 HETATM 21 O O3P UFP . . . O 3 75.68 75.452 269.163 1 90.93 ? O3P UFP 602 C 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 21 #