data_7XYJ # _model_server_result.job_id M9woJl5V4tm2mHs9tojPCw _model_server_result.datetime_utc '2024-11-23 19:20:08' _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 7xyj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":301}' # _entry.id 7XYJ # _exptl.entry_id 7XYJ _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 90 _cell.angle_gamma 90 _cell.entry_id 7XYJ _cell.length_a 54.91 _cell.length_b 132.35 _cell.length_c 234.11 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7XYJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,T,U 1 1 C,D,J,K,L,M,N,O,P,Q,R,S,V,W 2 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 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 H N N ? 2 J N N ? 2 Q 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 431 n n N1 C6 UMP sing 432 n n N1 C1' UMP sing 433 n n C2 N3 UMP sing 434 n n C2 O2 UMP doub 435 n n N3 C4 UMP sing 436 n n N3 HN3 UMP sing 437 n n C4 C5 UMP sing 438 n n C4 O4 UMP doub 439 n n C5 C6 UMP doub 440 n n C5 H5 UMP sing 441 n n C6 H6 UMP sing 442 n n C1' C2' UMP sing 443 n n C1' O4' UMP sing 444 n n C1' H1' UMP sing 445 n n C2' C3' UMP sing 446 n n C2' H2' UMP sing 447 n n C2' "H2''" UMP sing 448 n n C3' C4' UMP sing 449 n n C3' O3' UMP sing 450 n n C3' H3' UMP sing 451 n n C4' O4' UMP sing 452 n n C4' C5' UMP sing 453 n n C4' H4' UMP sing 454 n n O3' HO3' UMP sing 455 n n C5' O5' UMP sing 456 n n C5' H5' UMP sing 457 n n C5' "H5''" UMP sing 458 n n O5' P UMP sing 459 n n P OP1 UMP doub 460 n n P OP2 UMP sing 461 n n P OP3 UMP sing 462 n n OP2 HOP2 UMP sing 463 n n OP3 HOP3 UMP sing 464 n n # _atom_sites.entry_id 7XYJ _atom_sites.fract_transf_matrix[1][1] 0.018212 _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] 0.007556 _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] 0.004271 _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 1 301 301 UMP UMP . F 3 1PE A 1 302 302 1PE 1PE . G 4 SO4 A 1 303 303 SO4 SO4 . H 2 UMP B 1 301 301 UMP UMP . I 3 1PE B 1 302 302 1PE 1PE . J 2 UMP C 1 301 301 UMP UMP . K 3 1PE C 1 302 302 1PE 1PE . L 5 BTB C 1 303 303 BTB BTB . M 4 SO4 C 1 304 304 SO4 SO4 . N 4 SO4 C 1 305 305 SO4 SO4 . O 4 SO4 C 1 306 306 SO4 SO4 . P 4 SO4 C 1 307 304 SO4 SO4 . Q 2 UMP D 1 301 301 UMP UMP . R 3 1PE D 1 302 302 1PE 1PE . S 5 BTB D 1 303 303 BTB BTB . T 6 HOH A 1 401 169 HOH HOH . T 6 HOH A 2 402 22 HOH HOH . T 6 HOH A 3 403 12 HOH HOH . T 6 HOH A 4 404 88 HOH HOH . T 6 HOH A 5 405 36 HOH HOH . T 6 HOH A 6 406 90 HOH HOH . T 6 HOH A 7 407 185 HOH HOH . T 6 HOH A 8 408 23 HOH HOH . T 6 HOH A 9 409 126 HOH HOH . T 6 HOH A 10 410 59 HOH HOH . T 6 HOH A 11 411 53 HOH HOH . T 6 HOH A 12 412 130 HOH HOH . T 6 HOH A 13 413 81 HOH HOH . T 6 HOH A 14 414 119 HOH HOH . T 6 HOH A 15 415 167 HOH HOH . T 6 HOH A 16 416 107 HOH HOH . T 6 HOH A 17 417 137 HOH HOH . T 6 HOH A 18 418 138 HOH HOH . T 6 HOH A 19 419 62 HOH HOH . T 6 HOH A 20 420 5 HOH HOH . T 6 HOH A 21 421 60 HOH HOH . T 6 HOH A 22 422 162 HOH HOH . T 6 HOH A 23 423 129 HOH HOH . T 6 HOH A 24 424 184 HOH HOH . T 6 HOH A 25 425 47 HOH HOH . T 6 HOH A 26 426 21 HOH HOH . T 6 HOH A 27 427 154 HOH HOH . T 6 HOH A 28 428 149 HOH HOH . T 6 HOH A 29 429 170 HOH HOH . T 6 HOH A 30 430 69 HOH HOH . T 6 HOH A 31 431 133 HOH HOH . T 6 HOH A 32 432 93 HOH HOH . T 6 HOH A 33 433 152 HOH HOH . T 6 HOH A 34 434 168 HOH HOH . T 6 HOH A 35 435 102 HOH HOH . U 6 HOH B 1 401 34 HOH HOH . U 6 HOH B 2 402 141 HOH HOH . U 6 HOH B 3 403 37 HOH HOH . U 6 HOH B 4 404 10 HOH HOH . U 6 HOH B 5 405 72 HOH HOH . U 6 HOH B 6 406 2 HOH HOH . U 6 HOH B 7 407 114 HOH HOH . U 6 HOH B 8 408 193 HOH HOH . U 6 HOH B 9 409 71 HOH HOH . U 6 HOH B 10 410 38 HOH HOH . U 6 HOH B 11 411 139 HOH HOH . U 6 HOH B 12 412 131 HOH HOH . U 6 HOH B 13 413 123 HOH HOH . U 6 HOH B 14 414 29 HOH HOH . U 6 HOH B 15 415 32 HOH HOH . U 6 HOH B 16 416 26 HOH HOH . U 6 HOH B 17 417 164 HOH HOH . U 6 HOH B 18 418 174 HOH HOH . U 6 HOH B 19 419 118 HOH HOH . U 6 HOH B 20 420 159 HOH HOH . U 6 HOH B 21 421 35 HOH HOH . U 6 HOH B 22 422 43 HOH HOH . U 6 HOH B 23 423 1 HOH HOH . U 6 HOH B 24 424 177 HOH HOH . U 6 HOH B 25 425 142 HOH HOH . U 6 HOH B 26 426 161 HOH HOH . U 6 HOH B 27 427 150 HOH HOH . U 6 HOH B 28 428 111 HOH HOH . U 6 HOH B 29 429 191 HOH HOH . U 6 HOH B 30 430 27 HOH HOH . U 6 HOH B 31 431 9 HOH HOH . U 6 HOH B 32 432 86 HOH HOH . U 6 HOH B 33 433 144 HOH HOH . U 6 HOH B 34 434 79 HOH HOH . U 6 HOH B 35 435 112 HOH HOH . U 6 HOH B 36 436 187 HOH HOH . U 6 HOH B 37 437 146 HOH HOH . U 6 HOH B 38 438 63 HOH HOH . U 6 HOH B 39 439 163 HOH HOH . U 6 HOH B 40 440 160 HOH HOH . U 6 HOH B 41 441 153 HOH HOH . U 6 HOH B 42 442 97 HOH HOH . U 6 HOH B 43 443 44 HOH HOH . U 6 HOH B 44 444 135 HOH HOH . U 6 HOH B 45 445 140 HOH HOH . U 6 HOH B 46 446 28 HOH HOH . U 6 HOH B 47 447 165 HOH HOH . U 6 HOH B 48 448 156 HOH HOH . U 6 HOH B 49 449 124 HOH HOH . U 6 HOH B 50 450 74 HOH HOH . U 6 HOH B 51 451 76 HOH HOH . U 6 HOH B 52 452 103 HOH HOH . U 6 HOH B 53 453 173 HOH HOH . U 6 HOH B 54 454 73 HOH HOH . U 6 HOH B 55 455 178 HOH HOH . U 6 HOH B 56 456 109 HOH HOH . U 6 HOH B 57 457 58 HOH HOH . V 6 HOH C 1 401 17 HOH HOH . V 6 HOH C 2 402 75 HOH HOH . V 6 HOH C 3 403 40 HOH HOH . V 6 HOH C 4 404 84 HOH HOH . V 6 HOH C 5 405 20 HOH HOH . V 6 HOH C 6 406 66 HOH HOH . V 6 HOH C 7 407 95 HOH HOH . V 6 HOH C 8 408 18 HOH HOH . V 6 HOH C 9 409 145 HOH HOH . V 6 HOH C 10 410 91 HOH HOH . V 6 HOH C 11 411 68 HOH HOH . V 6 HOH C 12 412 19 HOH HOH . V 6 HOH C 13 413 190 HOH HOH . V 6 HOH C 14 414 188 HOH HOH . V 6 HOH C 15 415 186 HOH HOH . V 6 HOH C 16 416 33 HOH HOH . V 6 HOH C 17 417 77 HOH HOH . V 6 HOH C 18 418 8 HOH HOH . V 6 HOH C 19 419 104 HOH HOH . V 6 HOH C 20 420 166 HOH HOH . V 6 HOH C 21 421 101 HOH HOH . V 6 HOH C 22 422 182 HOH HOH . V 6 HOH C 23 423 113 HOH HOH . V 6 HOH C 24 424 7 HOH HOH . V 6 HOH C 25 425 155 HOH HOH . V 6 HOH C 26 426 31 HOH HOH . V 6 HOH C 27 427 78 HOH HOH . V 6 HOH C 28 428 143 HOH HOH . V 6 HOH C 29 429 67 HOH HOH . V 6 HOH C 30 430 157 HOH HOH . V 6 HOH C 31 431 51 HOH HOH . V 6 HOH C 32 432 183 HOH HOH . V 6 HOH C 33 433 106 HOH HOH . V 6 HOH C 34 434 127 HOH HOH . V 6 HOH C 35 435 110 HOH HOH . V 6 HOH C 36 436 181 HOH HOH . V 6 HOH C 37 437 147 HOH HOH . V 6 HOH C 38 438 158 HOH HOH . V 6 HOH C 39 439 49 HOH HOH . V 6 HOH C 40 440 176 HOH HOH . W 6 HOH D 1 401 172 HOH HOH . W 6 HOH D 2 402 115 HOH HOH . W 6 HOH D 3 403 25 HOH HOH . W 6 HOH D 4 404 3 HOH HOH . W 6 HOH D 5 405 13 HOH HOH . W 6 HOH D 6 406 4 HOH HOH . W 6 HOH D 7 407 39 HOH HOH . W 6 HOH D 8 408 56 HOH HOH . W 6 HOH D 9 409 189 HOH HOH . W 6 HOH D 10 410 48 HOH HOH . W 6 HOH D 11 411 57 HOH HOH . W 6 HOH D 12 412 50 HOH HOH . W 6 HOH D 13 413 42 HOH HOH . W 6 HOH D 14 414 6 HOH HOH . W 6 HOH D 15 415 96 HOH HOH . W 6 HOH D 16 416 30 HOH HOH . W 6 HOH D 17 417 15 HOH HOH . W 6 HOH D 18 418 61 HOH HOH . W 6 HOH D 19 419 87 HOH HOH . W 6 HOH D 20 420 194 HOH HOH . W 6 HOH D 21 421 148 HOH HOH . W 6 HOH D 22 422 100 HOH HOH . W 6 HOH D 23 423 151 HOH HOH . W 6 HOH D 24 424 54 HOH HOH . W 6 HOH D 25 425 92 HOH HOH . W 6 HOH D 26 426 70 HOH HOH . W 6 HOH D 27 427 98 HOH HOH . W 6 HOH D 28 428 11 HOH HOH . W 6 HOH D 29 429 120 HOH HOH . W 6 HOH D 30 430 80 HOH HOH . W 6 HOH D 31 431 89 HOH HOH . W 6 HOH D 32 432 16 HOH HOH . W 6 HOH D 33 433 65 HOH HOH . W 6 HOH D 34 434 99 HOH HOH . W 6 HOH D 35 435 82 HOH HOH . W 6 HOH D 36 436 116 HOH HOH . W 6 HOH D 37 437 132 HOH HOH . W 6 HOH D 38 438 24 HOH HOH . W 6 HOH D 39 439 179 HOH HOH . W 6 HOH D 40 440 121 HOH HOH . W 6 HOH D 41 441 128 HOH HOH . W 6 HOH D 42 442 41 HOH HOH . W 6 HOH D 43 443 64 HOH HOH . W 6 HOH D 44 444 14 HOH HOH . W 6 HOH D 45 445 94 HOH HOH . W 6 HOH D 46 446 85 HOH HOH . W 6 HOH D 47 447 105 HOH HOH . W 6 HOH D 48 448 122 HOH HOH . W 6 HOH D 49 449 55 HOH HOH . W 6 HOH D 50 450 125 HOH HOH . W 6 HOH D 51 451 108 HOH HOH . W 6 HOH D 52 452 52 HOH HOH . W 6 HOH D 53 453 46 HOH HOH . W 6 HOH D 54 454 171 HOH HOH . W 6 HOH D 55 455 134 HOH HOH . W 6 HOH D 56 456 192 HOH HOH . W 6 HOH D 57 457 136 HOH HOH . W 6 HOH D 58 458 180 HOH HOH . W 6 HOH D 59 459 83 HOH HOH . W 6 HOH D 60 460 117 HOH HOH . W 6 HOH D 61 461 45 HOH HOH . W 6 HOH D 62 462 175 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 . . . Q 2 7.161 -10.511 14.199 1 52.57 ? N1 UMP 301 D 1 HETATM 2 C C2 UMP . . . Q 2 8.064 -9.468 14.072 1 49.71 ? C2 UMP 301 D 1 HETATM 3 N N3 UMP . . . Q 2 7.508 -8.251 13.747 1 51.47 ? N3 UMP 301 D 1 HETATM 4 C C4 UMP . . . Q 2 6.167 -7.981 13.519 1 55.94 ? C4 UMP 301 D 1 HETATM 5 C C5 UMP . . . Q 2 5.291 -9.112 13.654 1 55.35 ? C5 UMP 301 D 1 HETATM 6 C C6 UMP . . . Q 2 5.801 -10.314 13.989 1 54.36 ? C6 UMP 301 D 1 HETATM 7 O O2 UMP . . . Q 2 9.272 -9.608 14.209 1 49.56 ? O2 UMP 301 D 1 HETATM 8 O O4 UMP . . . Q 2 5.819 -6.831 13.198 1 58 ? O4 UMP 301 D 1 HETATM 9 C C1' UMP . . . Q 2 7.694 -11.865 14.519 1 56.49 ? C1' UMP 301 D 1 HETATM 10 C C2' UMP . . . Q 2 8.082 -12.076 15.978 1 56.24 ? C2' UMP 301 D 1 HETATM 11 C C3' UMP . . . Q 2 7.843 -13.57 16.148 1 54.33 ? C3' UMP 301 D 1 HETATM 12 C C4' UMP . . . Q 2 6.594 -13.797 15.302 1 54.99 ? C4' UMP 301 D 1 HETATM 13 O O3' UMP . . . Q 2 8.904 -14.317 15.557 1 51.97 ? O3' UMP 301 D 1 HETATM 14 O O4' UMP . . . Q 2 6.675 -12.824 14.236 1 58.86 ? O4' UMP 301 D 1 HETATM 15 C C5' UMP . . . Q 2 5.282 -13.647 16.037 1 51.77 ? C5' UMP 301 D 1 HETATM 16 O O5' UMP . . . Q 2 5.18 -14.737 16.969 1 53.31 ? O5' UMP 301 D 1 HETATM 17 P P UMP . . . Q 2 4.681 -14.614 18.489 1 53.64 ? P UMP 301 D 1 HETATM 18 O OP1 UMP . . . Q 2 4.717 -15.966 19.094 1 55.82 ? OP1 UMP 301 D 1 HETATM 19 O OP2 UMP . . . Q 2 5.59 -13.64 19.214 1 54.91 ? OP2 UMP 301 D 1 HETATM 20 O OP3 UMP . . . Q 2 3.269 -13.978 18.452 1 53.5 ? OP3 UMP 301 D 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 20 #