data_6PF7 # _model_server_result.job_id OduIuRJb2xvrID1-bProzA _model_server_result.datetime_utc '2024-11-25 08:19:25' _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 6pf7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":602}' # _entry.id 6PF7 # _exptl.entry_id 6PF7 _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 94.68 _cell.angle_gamma 90 _cell.entry_id 6PF7 _cell.length_a 214.774 _cell.length_b 115.789 _cell.length_c 220.142 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PF7 _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,N,O,DA,EA 1 1 C,D,P,Q,R,S,T,U,V,W,X,Y,FA,GA 2 1 E,Z,AA,BA,CA,HA 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_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 196.81248 0 219.408031 # 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 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 6PF7 _atom_sites.fract_transf_matrix[1][1] 0.004656 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000381 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008636 _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] 0.004558 _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 OG7 A 1 603 603 OG7 TS1 . I 5 MTX A 1 604 604 MTX MTX . J 6 SO4 A 1 605 2 SO4 SO4 . K 2 NDP B 1 601 601 NDP NDP . L 3 UFP B 1 602 602 UFP UFP . M 4 OG7 B 1 603 603 OG7 TS1 . 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 OG7 C 1 603 603 OG7 TS1 . S 5 MTX C 1 604 604 MTX MTX . T 6 SO4 C 1 605 3 SO4 SO4 . U 2 NDP D 1 601 601 NDP NDP . V 3 UFP D 1 602 602 UFP UFP . W 4 OG7 D 1 603 603 OG7 TS1 . X 5 MTX D 1 604 604 MTX MTX . Y 6 SO4 D 1 605 4 SO4 SO4 . Z 2 NDP E 1 601 601 NDP NDP . AA 3 UFP E 1 602 602 UFP UFP . BA 4 OG7 E 1 603 603 OG7 TS1 . CA 5 MTX E 1 604 604 MTX MTX . DA 7 HOH A 1 701 74 HOH HOH . DA 7 HOH A 2 702 118 HOH HOH . DA 7 HOH A 3 703 51 HOH HOH . DA 7 HOH A 4 704 26 HOH HOH . DA 7 HOH A 5 705 56 HOH HOH . DA 7 HOH A 6 706 59 HOH HOH . DA 7 HOH A 7 707 64 HOH HOH . DA 7 HOH A 8 708 36 HOH HOH . DA 7 HOH A 9 709 32 HOH HOH . DA 7 HOH A 10 710 39 HOH HOH . DA 7 HOH A 11 711 58 HOH HOH . DA 7 HOH A 12 712 68 HOH HOH . DA 7 HOH A 13 713 114 HOH HOH . DA 7 HOH A 14 714 38 HOH HOH . DA 7 HOH A 15 715 53 HOH HOH . DA 7 HOH A 16 716 69 HOH HOH . DA 7 HOH A 17 717 37 HOH HOH . DA 7 HOH A 18 718 78 HOH HOH . DA 7 HOH A 19 719 107 HOH HOH . DA 7 HOH A 20 720 19 HOH HOH . DA 7 HOH A 21 721 132 HOH HOH . DA 7 HOH A 22 722 10 HOH HOH . DA 7 HOH A 23 723 17 HOH HOH . DA 7 HOH A 24 724 57 HOH HOH . DA 7 HOH A 25 725 12 HOH HOH . DA 7 HOH A 26 726 152 HOH HOH . DA 7 HOH A 27 727 3 HOH HOH . DA 7 HOH A 28 728 134 HOH HOH . DA 7 HOH A 29 729 7 HOH HOH . DA 7 HOH A 30 730 96 HOH HOH . DA 7 HOH A 31 731 135 HOH HOH . DA 7 HOH A 32 732 112 HOH HOH . DA 7 HOH A 33 733 133 HOH HOH . DA 7 HOH A 34 734 99 HOH HOH . DA 7 HOH A 35 735 111 HOH HOH . DA 7 HOH A 36 736 43 HOH HOH . DA 7 HOH A 37 737 4 HOH HOH . DA 7 HOH A 38 738 24 HOH HOH . DA 7 HOH A 39 739 66 HOH HOH . DA 7 HOH A 40 740 140 HOH HOH . DA 7 HOH A 41 741 23 HOH HOH . DA 7 HOH A 42 742 13 HOH HOH . DA 7 HOH A 43 743 5 HOH HOH . DA 7 HOH A 44 744 80 HOH HOH . DA 7 HOH A 45 745 142 HOH HOH . DA 7 HOH A 46 746 120 HOH HOH . DA 7 HOH A 47 747 82 HOH HOH . DA 7 HOH A 48 748 73 HOH HOH . DA 7 HOH A 49 749 93 HOH HOH . DA 7 HOH A 50 750 143 HOH HOH . DA 7 HOH A 51 751 117 HOH HOH . DA 7 HOH A 52 752 95 HOH HOH . DA 7 HOH A 53 753 122 HOH HOH . DA 7 HOH A 54 754 92 HOH HOH . DA 7 HOH A 55 755 75 HOH HOH . EA 7 HOH B 1 701 100 HOH HOH . EA 7 HOH B 2 702 89 HOH HOH . EA 7 HOH B 3 703 101 HOH HOH . EA 7 HOH B 4 704 54 HOH HOH . EA 7 HOH B 5 705 110 HOH HOH . EA 7 HOH B 6 706 18 HOH HOH . EA 7 HOH B 7 707 21 HOH HOH . EA 7 HOH B 8 708 87 HOH HOH . EA 7 HOH B 9 709 55 HOH HOH . EA 7 HOH B 10 710 50 HOH HOH . EA 7 HOH B 11 711 145 HOH HOH . EA 7 HOH B 12 712 81 HOH HOH . EA 7 HOH B 13 713 123 HOH HOH . EA 7 HOH B 14 714 14 HOH HOH . EA 7 HOH B 15 715 15 HOH HOH . EA 7 HOH B 16 716 45 HOH HOH . EA 7 HOH B 17 717 79 HOH HOH . EA 7 HOH B 18 718 131 HOH HOH . EA 7 HOH B 19 719 139 HOH HOH . EA 7 HOH B 20 720 128 HOH HOH . EA 7 HOH B 21 721 85 HOH HOH . EA 7 HOH B 22 722 130 HOH HOH . EA 7 HOH B 23 723 9 HOH HOH . EA 7 HOH B 24 724 47 HOH HOH . EA 7 HOH B 25 725 137 HOH HOH . EA 7 HOH B 26 726 91 HOH HOH . EA 7 HOH B 27 727 106 HOH HOH . FA 7 HOH C 1 701 121 HOH HOH . FA 7 HOH C 2 702 42 HOH HOH . FA 7 HOH C 3 703 102 HOH HOH . FA 7 HOH C 4 704 105 HOH HOH . FA 7 HOH C 5 705 94 HOH HOH . FA 7 HOH C 6 706 119 HOH HOH . FA 7 HOH C 7 707 70 HOH HOH . FA 7 HOH C 8 708 6 HOH HOH . FA 7 HOH C 9 709 49 HOH HOH . FA 7 HOH C 10 710 60 HOH HOH . FA 7 HOH C 11 711 46 HOH HOH . FA 7 HOH C 12 712 149 HOH HOH . FA 7 HOH C 13 713 71 HOH HOH . FA 7 HOH C 14 714 41 HOH HOH . FA 7 HOH C 15 715 84 HOH HOH . FA 7 HOH C 16 716 83 HOH HOH . FA 7 HOH C 17 717 76 HOH HOH . FA 7 HOH C 18 718 20 HOH HOH . FA 7 HOH C 19 719 8 HOH HOH . FA 7 HOH C 20 720 124 HOH HOH . FA 7 HOH C 21 721 2 HOH HOH . FA 7 HOH C 22 722 108 HOH HOH . FA 7 HOH C 23 723 138 HOH HOH . FA 7 HOH C 24 724 16 HOH HOH . FA 7 HOH C 25 725 126 HOH HOH . FA 7 HOH C 26 726 144 HOH HOH . FA 7 HOH C 27 727 104 HOH HOH . FA 7 HOH C 28 728 113 HOH HOH . GA 7 HOH D 1 701 125 HOH HOH . GA 7 HOH D 2 702 88 HOH HOH . GA 7 HOH D 3 703 67 HOH HOH . GA 7 HOH D 4 704 34 HOH HOH . GA 7 HOH D 5 705 44 HOH HOH . GA 7 HOH D 6 706 11 HOH HOH . GA 7 HOH D 7 707 115 HOH HOH . GA 7 HOH D 8 708 22 HOH HOH . GA 7 HOH D 9 709 25 HOH HOH . GA 7 HOH D 10 710 97 HOH HOH . GA 7 HOH D 11 711 109 HOH HOH . GA 7 HOH D 12 712 90 HOH HOH . GA 7 HOH D 13 713 147 HOH HOH . GA 7 HOH D 14 714 28 HOH HOH . GA 7 HOH D 15 715 63 HOH HOH . GA 7 HOH D 16 716 141 HOH HOH . GA 7 HOH D 17 717 77 HOH HOH . GA 7 HOH D 18 718 61 HOH HOH . GA 7 HOH D 19 719 86 HOH HOH . GA 7 HOH D 20 720 65 HOH HOH . GA 7 HOH D 21 721 1 HOH HOH . GA 7 HOH D 22 722 127 HOH HOH . GA 7 HOH D 23 723 148 HOH HOH . GA 7 HOH D 24 724 151 HOH HOH . GA 7 HOH D 25 725 72 HOH HOH . HA 7 HOH E 1 701 62 HOH HOH . HA 7 HOH E 2 702 52 HOH HOH . HA 7 HOH E 3 703 103 HOH HOH . HA 7 HOH E 4 704 150 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 . . . V 3 90.532 -53.019 44.491 1 102.75 ? N1 UFP 602 D 1 HETATM 2 C C2 UFP . . . V 3 89.185 -53.247 44.461 1 90.65 ? C2 UFP 602 D 1 HETATM 3 N N3 UFP . . . V 3 88.544 -53.412 43.285 1 94.03 ? N3 UFP 602 D 1 HETATM 4 C C4 UFP . . . V 3 89.202 -53.356 42.11 1 102.31 ? C4 UFP 602 D 1 HETATM 5 C C5 UFP . . . V 3 90.598 -53.119 42.12 1 105.74 ? C5 UFP 602 D 1 HETATM 6 C C6 UFP . . . V 3 91.219 -52.952 43.304 1 101.54 ? C6 UFP 602 D 1 HETATM 7 O O2 UFP . . . V 3 88.487 -53.315 45.46 1 85.17 ? O2 UFP 602 D 1 HETATM 8 O O4 UFP . . . V 3 88.61 -53.506 41.057 1 95.74 ? O4 UFP 602 D 1 HETATM 9 F F5 UFP . . . V 3 91.298 -53.056 40.962 1 100.5 ? F5 UFP 602 D 1 HETATM 10 C C1' UFP . . . V 3 91.37 -52.818 45.699 1 93.18 ? C1' UFP 602 D 1 HETATM 11 C C2' UFP . . . V 3 91.109 -53.784 46.879 1 80.61 ? C2' UFP 602 D 1 HETATM 12 C C3' UFP . . . V 3 92.405 -53.6 47.69 1 83.97 ? C3' UFP 602 D 1 HETATM 13 C C4' UFP . . . V 3 93.47 -53.485 46.582 1 87.96 ? C4' UFP 602 D 1 HETATM 14 O O3' UFP . . . V 3 92.362 -52.398 48.461 1 82.38 ? O3' UFP 602 D 1 HETATM 15 O O4' UFP . . . V 3 92.756 -53.099 45.371 1 88.89 ? O4' UFP 602 D 1 HETATM 16 C C5' UFP . . . V 3 94.205 -54.818 46.394 1 86.62 ? C5' UFP 602 D 1 HETATM 17 O O5' UFP . . . V 3 94.351 -55.47 47.658 1 67.95 ? O5' UFP 602 D 1 HETATM 18 P P UFP . . . V 3 95.616 -56.464 47.572 1 75.02 ? P UFP 602 D 1 HETATM 19 O O1P UFP . . . V 3 96.651 -55.909 46.476 1 84.22 ? O1P UFP 602 D 1 HETATM 20 O O2P UFP . . . V 3 96.271 -56.559 48.898 1 91.03 ? O2P UFP 602 D 1 HETATM 21 O O3P UFP . . . V 3 95.141 -57.93 47.132 1 71.89 ? O3P UFP 602 D 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #