data_1VQ2 # _model_server_result.job_id OopqQYVCcUWUJjacHjXu0g _model_server_result.datetime_utc '2024-10-11 06:19:35' _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 1vq2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":308}' # _entry.id 1VQ2 # _exptl.entry_id 1VQ2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 310.198 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3,4-DIHYDRO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 120 _cell.entry_id 1VQ2 _cell.length_a 114.528 _cell.length_b 114.528 _cell.length_c 76.95 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VQ2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 2' # 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 hexameric 6 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E 1 1,2 A,B,C,D,E 2 1,3,4,5,2,6 # 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' 11_655 -x+y+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 114.528 0 38.475 3 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 114.528 0 0 4 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 57.264 99.184157 0 5 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/2 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 57.264 99.184157 38.475 6 'crystal symmetry operation' 12_555 x,x-y,-z+1/2 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 38.475 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A SG CYS 19 A CYS 19 1_555 C ZN ZN . A ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc2 A SG CYS 49 A CYS 49 1_555 C ZN ZN . A ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc3 A NE2 HIS 94 A HIS 94 1_555 C ZN ZN . A ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc4 A OE2 GLU 102 A GLU 102 1_555 C ZN ZN . A ZN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc5 A ND1 HIS 104 A HIS 104 1_555 B ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc6 A SG CYS 132 A CYS 132 1_555 B ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc7 A SG CYS 135 A CYS 135 1_555 B ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc8 D O4 DDN . A DDN 308 1_555 B ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? # _chem_comp.formula 'C9 H15 N2 O8 P' _chem_comp.formula_weight 310.198 _chem_comp.id DDN _chem_comp.mon_nstd_flag n _chem_comp.name "3,4-DIHYDRO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _chem_comp.type 'dna linking' _chem_comp.pdbx_synonyms '((2R,3S,5R)-3-HYDROXY-5-(4-HYDROXY-2-OXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-TETRAHYDROFURAN-2-YL)METHYL DIHYDROGEN PHOSPHATE' # 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 OP3 P DDN doub 83 n n P OP1 DDN sing 84 n n P OP2 DDN sing 85 n n P O5' DDN sing 86 n n OP1 H1P DDN sing 87 n n OP2 H2P DDN sing 88 n n O5' C5' DDN sing 89 n n C5' C4' DDN sing 90 n n C5' H5' DDN sing 91 n n C5' "H5''" DDN sing 92 n n C4' O4' DDN sing 93 n n C4' C3' DDN sing 94 n n C4' H4' DDN sing 95 n n O4' C1' DDN sing 96 n n C3' O3' DDN sing 97 n n C3' C2' DDN sing 98 n n C3' H3' DDN sing 99 n n O3' H1 DDN sing 100 n n C2' C1' DDN sing 101 n n C2' H2' DDN sing 102 n n C2' "H2''" DDN sing 103 n n C1' N1 DDN sing 104 n n C1' H1' DDN sing 105 n n N1 C2 DDN sing 106 n n N1 C6 DDN sing 107 n n C2 O2 DDN doub 108 n n C2 N3 DDN sing 109 n n N3 C4 DDN sing 110 n n N3 HN3 DDN sing 111 n n C4 O4 DDN sing 112 n n C4 C5 DDN sing 113 n n C4 H4 DDN sing 114 n n O4 HO4 DDN sing 115 n n C5 C6 DDN doub 116 n n C5 H5 DDN sing 117 n n C6 H6 DDN sing 118 n n # _atom_sites.entry_id 1VQ2 _atom_sites.fract_transf_matrix[1][1] 0.008731 _atom_sites.fract_transf_matrix[1][2] 0.005041 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010082 _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] 0.012995 _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 B 2 ZN A 1 701 701 ZN ZN . C 2 ZN A 1 702 702 ZN ZN . D 3 DDN A 1 308 308 DDN DDN . E 4 HOH A 1 401 401 HOH HOH . E 4 HOH A 2 402 402 HOH HOH . E 4 HOH A 3 403 403 HOH HOH . E 4 HOH A 4 404 404 HOH HOH . E 4 HOH A 5 405 405 HOH HOH . E 4 HOH A 6 406 406 HOH HOH . E 4 HOH A 7 407 407 HOH HOH . E 4 HOH A 8 408 408 HOH HOH . E 4 HOH A 9 409 409 HOH HOH . E 4 HOH A 10 410 410 HOH HOH . E 4 HOH A 11 411 411 HOH HOH . E 4 HOH A 12 412 412 HOH HOH . E 4 HOH A 13 413 413 HOH HOH . E 4 HOH A 14 414 414 HOH HOH . E 4 HOH A 15 415 415 HOH HOH . E 4 HOH A 16 416 416 HOH HOH . E 4 HOH A 17 417 417 HOH HOH . E 4 HOH A 18 418 418 HOH HOH . E 4 HOH A 19 419 419 HOH HOH . E 4 HOH A 20 420 420 HOH HOH . E 4 HOH A 21 421 421 HOH HOH . E 4 HOH A 22 422 422 HOH HOH . E 4 HOH A 23 423 423 HOH HOH . E 4 HOH A 24 424 424 HOH HOH . E 4 HOH A 25 425 425 HOH HOH . E 4 HOH A 26 426 426 HOH HOH . E 4 HOH A 27 427 427 HOH HOH . E 4 HOH A 28 428 428 HOH HOH . E 4 HOH A 29 429 429 HOH HOH . E 4 HOH A 30 430 430 HOH HOH . E 4 HOH A 31 431 431 HOH HOH . E 4 HOH A 32 432 432 HOH HOH . E 4 HOH A 33 433 433 HOH HOH . E 4 HOH A 34 434 434 HOH HOH . E 4 HOH A 35 435 435 HOH HOH . E 4 HOH A 36 436 436 HOH HOH . E 4 HOH A 37 437 437 HOH HOH . E 4 HOH A 38 438 438 HOH HOH . E 4 HOH A 39 439 439 HOH HOH . E 4 HOH A 40 440 440 HOH HOH . E 4 HOH A 41 441 441 HOH HOH . E 4 HOH A 42 442 442 HOH HOH . E 4 HOH A 43 443 443 HOH HOH . E 4 HOH A 44 444 444 HOH HOH . E 4 HOH A 45 445 445 HOH HOH . E 4 HOH A 46 446 446 HOH HOH . E 4 HOH A 47 447 447 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 OP3 DDN . . . D 3 81.603 5.502 15.525 1 46.03 ? OP3 DDN 308 A 1 HETATM 2 P P DDN . . . D 3 81.104 6.559 16.5 1 45.71 ? P DDN 308 A 1 HETATM 3 O OP1 DDN . . . D 3 81.184 6.11 17.93 1 45.99 ? OP1 DDN 308 A 1 HETATM 4 O OP2 DDN . . . D 3 81.744 7.909 16.231 1 45.15 ? OP2 DDN 308 A 1 HETATM 5 O O5' DDN . . . D 3 79.511 6.767 16.211 1 44.82 ? O5' DDN 308 A 1 HETATM 6 C C5' DDN . . . D 3 78.688 7.541 17.107 1 43.57 ? C5' DDN 308 A 1 HETATM 7 C C4' DDN . . . D 3 77.479 8.062 16.349 1 42.26 ? C4' DDN 308 A 1 HETATM 8 O O4' DDN . . . D 3 76.41 8.4 17.232 1 41.29 ? O4' DDN 308 A 1 HETATM 9 C C3' DDN . . . D 3 77.747 9.312 15.493 1 42.24 ? C3' DDN 308 A 1 HETATM 10 O O3' DDN . . . D 3 76.949 9.301 14.345 1 42.06 ? O3' DDN 308 A 1 HETATM 11 C C2' DDN . . . D 3 77.415 10.49 16.322 1 41.86 ? C2' DDN 308 A 1 HETATM 12 C C1' DDN . . . D 3 76.539 9.824 17.34 1 40.93 ? C1' DDN 308 A 1 HETATM 13 N N1 DDN . . . D 3 75.921 9.989 18.846 1 40.78 ? N1 DDN 308 A 1 HETATM 14 C C2 DDN . . . D 3 74.822 10.856 19.02 1 39.81 ? C2 DDN 308 A 1 HETATM 15 O O2 DDN . . . D 3 74.237 11.417 18.093 1 39.09 ? O2 DDN 308 A 1 HETATM 16 N N3 DDN . . . D 3 74.538 11.168 20.353 1 39.5 ? N3 DDN 308 A 1 HETATM 17 C C4 DDN . . . D 3 75.573 10.985 21.525 1 39.11 ? C4 DDN 308 A 1 HETATM 18 O O4 DDN . . . D 3 76.02 12.231 22.079 1 35.99 ? O4 DDN 308 A 1 HETATM 19 C C5 DDN . . . D 3 76.84 10.235 21.035 1 39.1 ? C5 DDN 308 A 1 HETATM 20 C C6 DDN . . . D 3 76.985 9.896 19.719 1 39.43 ? C6 DDN 308 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 20 #