data_6PFE # _model_server_result.job_id zAgNW-FWEkHNGx4f6U8zSA _model_server_result.datetime_utc '2024-11-13 12:50:55' _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 6pfe # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":602}' # _entry.id 6PFE # _exptl.entry_id 6PFE _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 _cell.angle_gamma 90 _cell.entry_id 6PFE _cell.length_a 212.859 _cell.length_b 115.641 _cell.length_c 219.899 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PFE _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,Z,AA 1 1 C,E,N,O,P,Q,V,W,X,Y,BA,DA 2 1 D,R,S,T,U,CA 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_558 -x,y,-z+3 -1 0 0 0 1 0 0 0 -1 -57.496382 0 657.186654 # 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 6PFE _atom_sites.fract_transf_matrix[1][1] 0.004698 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000411 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008647 _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] 0.004565 _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 OEA A 1 603 603 OEA T12 . 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 OEA B 1 603 603 OEA T12 . 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 OEA C 1 603 603 OEA T12 . 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 OEA D 1 603 603 OEA T12 . 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 OEA E 1 603 603 OEA T12 . Y 5 MTX E 1 604 604 MTX MTX . Z 6 HOH A 1 701 29 HOH HOH . Z 6 HOH A 2 702 21 HOH HOH . Z 6 HOH A 3 703 40 HOH HOH . Z 6 HOH A 4 704 17 HOH HOH . Z 6 HOH A 5 705 15 HOH HOH . Z 6 HOH A 6 706 2 HOH HOH . Z 6 HOH A 7 707 20 HOH HOH . Z 6 HOH A 8 708 25 HOH HOH . Z 6 HOH A 9 709 3 HOH HOH . AA 6 HOH B 1 701 18 HOH HOH . AA 6 HOH B 2 702 31 HOH HOH . AA 6 HOH B 3 703 23 HOH HOH . AA 6 HOH B 4 704 16 HOH HOH . AA 6 HOH B 5 705 19 HOH HOH . AA 6 HOH B 6 706 8 HOH HOH . AA 6 HOH B 7 707 27 HOH HOH . AA 6 HOH B 8 708 4 HOH HOH . AA 6 HOH B 9 709 11 HOH HOH . AA 6 HOH B 10 710 30 HOH HOH . AA 6 HOH B 11 711 13 HOH HOH . AA 6 HOH B 12 712 1 HOH HOH . AA 6 HOH B 13 713 14 HOH HOH . AA 6 HOH B 14 714 34 HOH HOH . BA 6 HOH C 1 701 33 HOH HOH . BA 6 HOH C 2 702 43 HOH HOH . BA 6 HOH C 3 703 35 HOH HOH . BA 6 HOH C 4 704 39 HOH HOH . BA 6 HOH C 5 705 9 HOH HOH . CA 6 HOH D 1 701 22 HOH HOH . CA 6 HOH D 2 702 42 HOH HOH . CA 6 HOH D 3 703 5 HOH HOH . DA 6 HOH E 1 701 26 HOH HOH . DA 6 HOH E 2 702 32 HOH HOH . DA 6 HOH E 3 703 28 HOH HOH . DA 6 HOH E 4 704 36 HOH HOH . DA 6 HOH E 5 705 12 HOH HOH . DA 6 HOH E 6 706 10 HOH HOH . DA 6 HOH E 7 707 41 HOH HOH . DA 6 HOH E 8 708 24 HOH HOH . DA 6 HOH E 9 709 6 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 . . . O 3 56.744 51.411 262.05 1 77.15 ? N1 UFP 602 C 1 HETATM 2 C C2 UFP . . . O 3 56.971 52.183 263.15 1 72.64 ? C2 UFP 602 C 1 HETATM 3 N N3 UFP . . . O 3 58.124 52.057 263.839 1 72.19 ? N3 UFP 602 C 1 HETATM 4 C C4 UFP . . . O 3 59.074 51.176 263.469 1 67.3 ? C4 UFP 602 C 1 HETATM 5 C C5 UFP . . . O 3 58.848 50.366 262.327 1 66.46 ? C5 UFP 602 C 1 HETATM 6 C C6 UFP . . . O 3 57.693 50.504 261.661 1 71.95 ? C6 UFP 602 C 1 HETATM 7 O O2 UFP . . . O 3 56.175 53.009 263.572 1 63.39 ? O2 UFP 602 C 1 HETATM 8 O O4 UFP . . . O 3 60.102 51.081 264.112 1 74.4 ? O4 UFP 602 C 1 HETATM 9 F F5 UFP . . . O 3 59.754 49.46 261.896 1 67.41 ? F5 UFP 602 C 1 HETATM 10 C C1' UFP . . . O 3 55.553 51.422 261.177 1 67.36 ? C1' UFP 602 C 1 HETATM 11 C C2' UFP . . . O 3 55.084 52.823 260.724 1 61.69 ? C2' UFP 602 C 1 HETATM 12 C C3' UFP . . . O 3 54.298 52.483 259.443 1 57.41 ? C3' UFP 602 C 1 HETATM 13 C C4' UFP . . . O 3 55.129 51.337 258.838 1 61.66 ? C4' UFP 602 C 1 HETATM 14 O O3' UFP . . . O 3 52.986 52.004 259.744 1 60.32 ? O3' UFP 602 C 1 HETATM 15 O O4' UFP . . . O 3 55.929 50.794 259.926 1 73.83 ? O4' UFP 602 C 1 HETATM 16 C C5' UFP . . . O 3 56 51.848 257.686 1 57.18 ? C5' UFP 602 C 1 HETATM 17 O O5' UFP . . . O 3 55.119 52.201 256.621 1 63.27 ? O5' UFP 602 C 1 HETATM 18 P P UFP . . . O 3 55.77 53.385 255.75 1 69.54 ? P UFP 602 C 1 HETATM 19 O O1P UFP . . . O 3 55.041 53.365 254.319 1 71.27 ? O1P UFP 602 C 1 HETATM 20 O O2P UFP . . . O 3 55.524 54.69 256.399 1 55.83 ? O2P UFP 602 C 1 HETATM 21 O O3P UFP . . . O 3 57.353 53.176 255.567 1 59.83 ? O3P UFP 602 C 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #