data_6PF5 # _model_server_result.job_id flT82VL4B7Hz8utT9A0nIA _model_server_result.datetime_utc '2024-11-28 08:10:07' _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 6pf5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":600}' # _entry.id 6PF5 # _exptl.entry_id 6PF5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 89.93 _cell.angle_gamma 90 _cell.entry_id 6PF5 _cell.length_a 85.155 _cell.length_b 85.134 _cell.length_c 175.744 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PF5 _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,E,F,M 1 1 D,K,L,P 1 4 B,G,H,N 2 1,2 C,I,J,O 3 1,3 # 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_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -85.155 0 0 3 'crystal symmetry operation' 2_456 -x-1,y,-z+1 -1 0 0 0 1 0 0 0 -1 -84.940288 0 175.743869 4 'crystal symmetry operation' 3_445 x-1/2,y-1/2,z 1 0 0 0 1 0 0 0 1 -42.5775 -42.567 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 G N N ? 2 I N N ? 2 K N N # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 UMP sing 415 n n N1 C6 UMP sing 416 n n N1 C1' UMP sing 417 n n C2 N3 UMP sing 418 n n C2 O2 UMP doub 419 n n N3 C4 UMP sing 420 n n N3 HN3 UMP sing 421 n n C4 C5 UMP sing 422 n n C4 O4 UMP doub 423 n n C5 C6 UMP doub 424 n n C5 H5 UMP sing 425 n n C6 H6 UMP sing 426 n n C1' C2' UMP sing 427 n n C1' O4' UMP sing 428 n n C1' H1' UMP sing 429 n n C2' C3' UMP sing 430 n n C2' H2' UMP sing 431 n n C2' "H2''" UMP sing 432 n n C3' C4' UMP sing 433 n n C3' O3' UMP sing 434 n n C3' H3' UMP sing 435 n n C4' O4' UMP sing 436 n n C4' C5' UMP sing 437 n n C4' H4' UMP sing 438 n n O3' HO3' UMP sing 439 n n C5' O5' UMP sing 440 n n C5' H5' UMP sing 441 n n C5' "H5''" UMP sing 442 n n O5' P UMP sing 443 n n P OP1 UMP doub 444 n n P OP2 UMP sing 445 n n P OP3 UMP sing 446 n n OP2 HOP2 UMP sing 447 n n OP3 HOP3 UMP sing 448 n n # _atom_sites.entry_id 6PF5 _atom_sites.fract_transf_matrix[1][1] 0.011743 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] -0.000015 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011746 _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] 0.00569 _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 E 2 UMP A 1 600 600 UMP UMP . F 3 OED A 1 601 601 OED T10 . G 2 UMP B 1 600 600 UMP UMP . H 3 OED B 1 601 601 OED T10 . I 2 UMP C 1 600 600 UMP UMP . J 3 OED C 1 601 601 OED T10 . K 2 UMP D 1 600 600 UMP UMP . L 3 OED D 1 601 601 OED T10 . M 4 HOH A 1 701 22 HOH HOH . M 4 HOH A 2 702 83 HOH HOH . M 4 HOH A 3 703 55 HOH HOH . M 4 HOH A 4 704 20 HOH HOH . M 4 HOH A 5 705 14 HOH HOH . M 4 HOH A 6 706 45 HOH HOH . M 4 HOH A 7 707 8 HOH HOH . M 4 HOH A 8 708 24 HOH HOH . M 4 HOH A 9 709 114 HOH HOH . M 4 HOH A 10 710 49 HOH HOH . M 4 HOH A 11 711 52 HOH HOH . M 4 HOH A 12 712 79 HOH HOH . M 4 HOH A 13 713 101 HOH HOH . M 4 HOH A 14 714 5 HOH HOH . M 4 HOH A 15 715 69 HOH HOH . M 4 HOH A 16 716 34 HOH HOH . M 4 HOH A 17 717 73 HOH HOH . M 4 HOH A 18 718 123 HOH HOH . M 4 HOH A 19 719 11 HOH HOH . M 4 HOH A 20 720 90 HOH HOH . M 4 HOH A 21 721 47 HOH HOH . M 4 HOH A 22 722 41 HOH HOH . M 4 HOH A 23 723 9 HOH HOH . M 4 HOH A 24 724 112 HOH HOH . M 4 HOH A 25 725 128 HOH HOH . M 4 HOH A 26 726 109 HOH HOH . M 4 HOH A 27 727 42 HOH HOH . M 4 HOH A 28 728 40 HOH HOH . N 4 HOH B 1 701 127 HOH HOH . N 4 HOH B 2 702 75 HOH HOH . N 4 HOH B 3 703 29 HOH HOH . N 4 HOH B 4 704 33 HOH HOH . N 4 HOH B 5 705 12 HOH HOH . N 4 HOH B 6 706 98 HOH HOH . N 4 HOH B 7 707 10 HOH HOH . N 4 HOH B 8 708 96 HOH HOH . N 4 HOH B 9 709 56 HOH HOH . N 4 HOH B 10 710 119 HOH HOH . N 4 HOH B 11 711 36 HOH HOH . N 4 HOH B 12 712 43 HOH HOH . N 4 HOH B 13 713 64 HOH HOH . N 4 HOH B 14 714 113 HOH HOH . N 4 HOH B 15 715 60 HOH HOH . N 4 HOH B 16 716 28 HOH HOH . N 4 HOH B 17 717 7 HOH HOH . N 4 HOH B 18 718 103 HOH HOH . N 4 HOH B 19 719 26 HOH HOH . N 4 HOH B 20 720 63 HOH HOH . N 4 HOH B 21 721 97 HOH HOH . N 4 HOH B 22 722 80 HOH HOH . N 4 HOH B 23 723 19 HOH HOH . N 4 HOH B 24 724 81 HOH HOH . N 4 HOH B 25 725 95 HOH HOH . N 4 HOH B 26 726 68 HOH HOH . N 4 HOH B 27 727 116 HOH HOH . N 4 HOH B 28 728 21 HOH HOH . N 4 HOH B 29 729 72 HOH HOH . N 4 HOH B 30 730 89 HOH HOH . N 4 HOH B 31 731 108 HOH HOH . N 4 HOH B 32 732 126 HOH HOH . N 4 HOH B 33 733 99 HOH HOH . N 4 HOH B 34 734 88 HOH HOH . O 4 HOH C 1 701 35 HOH HOH . O 4 HOH C 2 702 91 HOH HOH . O 4 HOH C 3 703 107 HOH HOH . O 4 HOH C 4 704 17 HOH HOH . O 4 HOH C 5 705 15 HOH HOH . O 4 HOH C 6 706 44 HOH HOH . O 4 HOH C 7 707 48 HOH HOH . O 4 HOH C 8 708 66 HOH HOH . O 4 HOH C 9 709 86 HOH HOH . O 4 HOH C 10 710 4 HOH HOH . O 4 HOH C 11 711 105 HOH HOH . O 4 HOH C 12 712 61 HOH HOH . O 4 HOH C 13 713 54 HOH HOH . O 4 HOH C 14 714 62 HOH HOH . O 4 HOH C 15 715 87 HOH HOH . O 4 HOH C 16 716 3 HOH HOH . O 4 HOH C 17 717 78 HOH HOH . O 4 HOH C 18 718 106 HOH HOH . O 4 HOH C 19 719 94 HOH HOH . O 4 HOH C 20 720 39 HOH HOH . O 4 HOH C 21 721 118 HOH HOH . O 4 HOH C 22 722 84 HOH HOH . O 4 HOH C 23 723 37 HOH HOH . O 4 HOH C 24 724 57 HOH HOH . O 4 HOH C 25 725 18 HOH HOH . O 4 HOH C 26 726 82 HOH HOH . O 4 HOH C 27 727 65 HOH HOH . O 4 HOH C 28 728 50 HOH HOH . O 4 HOH C 29 729 32 HOH HOH . O 4 HOH C 30 730 53 HOH HOH . O 4 HOH C 31 731 85 HOH HOH . O 4 HOH C 32 732 102 HOH HOH . O 4 HOH C 33 733 117 HOH HOH . P 4 HOH D 1 701 31 HOH HOH . P 4 HOH D 2 702 93 HOH HOH . P 4 HOH D 3 703 115 HOH HOH . P 4 HOH D 4 704 13 HOH HOH . P 4 HOH D 5 705 121 HOH HOH . P 4 HOH D 6 706 27 HOH HOH . P 4 HOH D 7 707 23 HOH HOH . P 4 HOH D 8 708 67 HOH HOH . P 4 HOH D 9 709 70 HOH HOH . P 4 HOH D 10 710 111 HOH HOH . P 4 HOH D 11 711 104 HOH HOH . P 4 HOH D 12 712 92 HOH HOH . P 4 HOH D 13 713 100 HOH HOH . P 4 HOH D 14 714 58 HOH HOH . P 4 HOH D 15 715 77 HOH HOH . P 4 HOH D 16 716 110 HOH HOH . P 4 HOH D 17 717 1 HOH HOH . P 4 HOH D 18 718 46 HOH HOH . P 4 HOH D 19 719 2 HOH HOH . P 4 HOH D 20 720 38 HOH HOH . P 4 HOH D 21 721 16 HOH HOH . P 4 HOH D 22 722 30 HOH HOH . P 4 HOH D 23 723 51 HOH HOH . P 4 HOH D 24 724 71 HOH HOH . P 4 HOH D 25 725 76 HOH HOH . P 4 HOH D 26 726 6 HOH HOH . P 4 HOH D 27 727 74 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 UMP . . . K 2 4.832 21.326 58.302 1 45.13 ? N1 UMP 600 D 1 HETATM 2 C C2 UMP . . . K 2 5.759 20.846 57.345 1 43.61 ? C2 UMP 600 D 1 HETATM 3 N N3 UMP . . . K 2 5.277 19.967 56.375 1 43.97 ? N3 UMP 600 D 1 HETATM 4 C C4 UMP . . . K 2 3.962 19.514 56.264 1 44.54 ? C4 UMP 600 D 1 HETATM 5 C C5 UMP . . . K 2 3.058 20.041 57.28 1 47.74 ? C5 UMP 600 D 1 HETATM 6 C C6 UMP . . . K 2 3.514 20.894 58.23 1 47.98 ? C6 UMP 600 D 1 HETATM 7 O O2 UMP . . . K 2 6.947 21.165 57.329 1 41.39 ? O2 UMP 600 D 1 HETATM 8 O O4 UMP . . . K 2 3.65 18.734 55.366 1 42.87 ? O4 UMP 600 D 1 HETATM 9 C C1' UMP . . . K 2 5.257 22.284 59.396 1 44.22 ? C1' UMP 600 D 1 HETATM 10 C C2' UMP . . . K 2 5.729 23.657 58.9 1 40.63 ? C2' UMP 600 D 1 HETATM 11 C C3' UMP . . . K 2 5.429 24.496 60.131 1 41.05 ? C3' UMP 600 D 1 HETATM 12 C C4' UMP . . . K 2 4.133 23.877 60.668 1 40.1 ? C4' UMP 600 D 1 HETATM 13 O O3' UMP . . . K 2 6.483 24.406 61.067 1 38.67 ? O3' UMP 600 D 1 HETATM 14 O O4' UMP . . . K 2 4.161 22.52 60.224 1 43.77 ? O4' UMP 600 D 1 HETATM 15 C C5' UMP . . . K 2 2.86 24.573 60.151 1 42.67 ? C5' UMP 600 D 1 HETATM 16 O O5' UMP . . . K 2 2.64 25.854 60.719 1 46.08 ? O5' UMP 600 D 1 HETATM 17 P P UMP . . . K 2 2.254 27.157 59.823 1 46.46 ? P UMP 600 D 1 HETATM 18 O OP1 UMP . . . K 2 3.273 27.599 58.832 1 47.56 ? OP1 UMP 600 D 1 HETATM 19 O OP2 UMP . . . K 2 0.817 26.729 59.209 1 43.83 -1 OP2 UMP 600 D 1 HETATM 20 O OP3 UMP . . . K 2 1.851 28.251 60.949 1 53.2 -1 OP3 UMP 600 D 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #