data_7K1O # _model_server_result.job_id 2TQWwOgD2TZXkey4rYiuMg _model_server_result.datetime_utc '2024-11-08 15:59:55' _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 7k1o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 7K1O # _exptl.entry_id 7K1O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-(3,5-di-O-phosphono-alpha-L-xylofuranosyl)pyrimidine-2,4(1H,3H)-dione _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 7K1O _cell.length_a 87.46 _cell.length_b 151.321 _cell.length_c 197.518 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7K1O _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall 'C 2c 2' _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 3_654 -x+1,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 87.46 0 -98.759 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 F N N ? 2 H N N # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id VQV _chem_comp.mon_nstd_flag . _chem_comp.name 1-(3,5-di-O-phosphono-alpha-L-xylofuranosyl)pyrimidine-2,4(1H,3H)-dione _chem_comp.type non-polymer _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 O3P P VQV doub 385 n n P O1P VQV sing 386 n n P O5' VQV sing 387 n n P O2P VQV sing 388 n n O5' C5' VQV sing 389 n n C5' C4' VQV sing 390 n n O4' C4' VQV sing 391 n n O4' C1' VQV sing 392 n n C4' C3' VQV sing 393 n n C6 C5 VQV doub 394 n n C6 N1 VQV sing 395 n n C5 C4 VQV sing 396 n n C1' N1 VQV sing 397 n n C1' C2' VQV sing 398 n n N1 C2 VQV sing 399 n n O2B P2 VQV doub 400 n n C4 O4 VQV doub 401 n n C4 N3 VQV sing 402 n n C3' O3' VQV sing 403 n n C3' C2' VQV sing 404 n n O3' P2 VQV sing 405 n n C2' O2' VQV sing 406 n n C2 N3 VQV sing 407 n n C2 O2 VQV doub 408 n n P2 O2C VQV sing 409 n n P2 O2A VQV sing 410 n n C6 H1 VQV sing 411 n n C5 H2 VQV sing 412 n n C1' H3 VQV sing 413 n n C2' H4 VQV sing 414 n n C3' H5 VQV sing 415 n n C4' H6 VQV sing 416 n n C5' H7 VQV sing 417 n n C5' H8 VQV sing 418 n n N3 H9 VQV sing 419 n n O1P H10 VQV sing 420 n n O2' H11 VQV sing 421 n n O2A H12 VQV sing 422 n n O2C H13 VQV sing 423 n n O2P H14 VQV sing 424 n n # _atom_sites.entry_id 7K1O _atom_sites.fract_transf_matrix[1][1] 0.011434 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006608 _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] 0.005063 _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 D 2 VQV A 1 401 401 VQV U53 . E 3 EDO A 1 402 501 EDO EDO . F 2 VQV B 1 401 401 VQV U53 . G 3 EDO B 1 402 501 EDO EDO . H 2 VQV C 1 401 401 VQV U53 . I 3 EDO C 1 402 501 EDO EDO . J 4 HOH A 1 501 20 HOH HOH . J 4 HOH A 2 502 16 HOH HOH . J 4 HOH A 3 503 17 HOH HOH . J 4 HOH A 4 504 12 HOH HOH . J 4 HOH A 5 505 2 HOH HOH . J 4 HOH A 6 506 8 HOH HOH . J 4 HOH A 7 507 31 HOH HOH . J 4 HOH A 8 508 9 HOH HOH . J 4 HOH A 9 509 38 HOH HOH . J 4 HOH A 10 510 35 HOH HOH . J 4 HOH A 11 511 52 HOH HOH . J 4 HOH A 12 512 29 HOH HOH . J 4 HOH A 13 513 53 HOH HOH . J 4 HOH A 14 514 40 HOH HOH . J 4 HOH A 15 515 24 HOH HOH . J 4 HOH A 16 516 18 HOH HOH . J 4 HOH A 17 517 7 HOH HOH . J 4 HOH A 18 518 34 HOH HOH . J 4 HOH A 19 519 6 HOH HOH . J 4 HOH A 20 520 54 HOH HOH . J 4 HOH A 21 521 41 HOH HOH . K 4 HOH B 1 501 14 HOH HOH . K 4 HOH B 2 502 45 HOH HOH . K 4 HOH B 3 503 32 HOH HOH . K 4 HOH B 4 504 47 HOH HOH . K 4 HOH B 5 505 43 HOH HOH . K 4 HOH B 6 506 37 HOH HOH . K 4 HOH B 7 507 30 HOH HOH . K 4 HOH B 8 508 26 HOH HOH . K 4 HOH B 9 509 36 HOH HOH . K 4 HOH B 10 510 39 HOH HOH . K 4 HOH B 11 511 19 HOH HOH . L 4 HOH C 1 501 46 HOH HOH . L 4 HOH C 2 502 21 HOH HOH . L 4 HOH C 3 503 50 HOH HOH . L 4 HOH C 4 504 5 HOH HOH . L 4 HOH C 5 505 10 HOH HOH . L 4 HOH C 6 506 44 HOH HOH . L 4 HOH C 7 507 51 HOH HOH . L 4 HOH C 8 508 4 HOH HOH . L 4 HOH C 9 509 49 HOH HOH . L 4 HOH C 10 510 48 HOH HOH . L 4 HOH C 11 511 25 HOH HOH . L 4 HOH C 12 512 33 HOH HOH . L 4 HOH C 13 513 27 HOH HOH . L 4 HOH C 14 514 22 HOH HOH . L 4 HOH C 15 515 42 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 O O2 VQV . . . D 2 33.757 1.712 -19.237 0.9 102.99 ? O2 VQV 401 A 1 HETATM 2 N N1 VQV . . . D 2 34.996 2.101 -21.07 0.9 102.93 ? N1 VQV 401 A 1 HETATM 3 C C4 VQV . . . D 2 35.791 -0.515 -20.976 0.9 106.57 ? C4 VQV 401 A 1 HETATM 4 C C2 VQV . . . D 2 34.548 1.28 -20.104 0.9 104.21 ? C2 VQV 401 A 1 HETATM 5 C C6 VQV . . . D 2 35.84 1.641 -22.004 0.9 103.23 ? C6 VQV 401 A 1 HETATM 6 C C5 VQV . . . D 2 36.262 0.317 -21.98 0.9 103.44 ? C5 VQV 401 A 1 HETATM 7 C C1' VQV . . . D 2 34.558 3.507 -21.113 0.9 97.96 ? C1' VQV 401 A 1 HETATM 8 C C2' VQV . . . D 2 35.332 4.389 -20.131 0.9 92.73 ? C2' VQV 401 A 1 HETATM 9 C C3' VQV . . . D 2 35.578 5.676 -20.888 0.9 89.59 ? C3' VQV 401 A 1 HETATM 10 C C4' VQV . . . D 2 35.628 5.199 -22.328 0.9 91.06 ? C4' VQV 401 A 1 HETATM 11 C C5' VQV . . . D 2 35.21 6.258 -23.332 0.9 89 ? C5' VQV 401 A 1 HETATM 12 N N3 VQV . . . D 2 34.939 -0.017 -20.053 0.9 107.49 ? N3 VQV 401 A 1 HETATM 13 O O1P VQV . . . D 2 37.487 4.116 -24.712 0.9 99.1 ? O1P VQV 401 A 1 HETATM 14 O O2' VQV . . . D 2 36.609 3.805 -19.844 0.9 96.05 ? O2' VQV 401 A 1 HETATM 15 O O2A VQV . . . D 2 33.467 8.2 -19.054 0.9 75.83 ? O2A VQV 401 A 1 HETATM 16 O O2B VQV . . . D 2 34.68 9.072 -21.011 0.9 75.09 ? O2B VQV 401 A 1 HETATM 17 O O2C VQV . . . D 2 35.94 7.998 -19.177 0.9 75.83 ? O2C VQV 401 A 1 HETATM 18 O O2P VQV . . . D 2 37.971 6.488 -24.257 0.9 95.7 ? O2P VQV 401 A 1 HETATM 19 O O3' VQV . . . D 2 34.479 6.558 -20.688 0.9 84.59 ? O3' VQV 401 A 1 HETATM 20 O O3P VQV . . . D 2 37.236 5.785 -26.52 0.9 95.25 ? O3P VQV 401 A 1 HETATM 21 O O4 VQV . . . D 2 36.187 -1.818 -20.925 0.9 106.74 ? O4 VQV 401 A 1 HETATM 22 O O4' VQV . . . D 2 34.759 4.068 -22.417 0.9 94.49 ? O4' VQV 401 A 1 HETATM 23 O O5' VQV . . . D 2 35.556 5.792 -24.632 0.9 93.57 ? O5' VQV 401 A 1 HETATM 24 P P VQV . . . D 2 37.096 5.534 -25.037 0.9 98.84 ? P VQV 401 A 1 HETATM 25 P P2 VQV . . . D 2 34.65 7.988 -19.965 0.9 74.62 ? P2 VQV 401 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 25 #