data_4HO8 # _model_server_result.job_id l9i7gW2NGiZThY_qb0i-Pg _model_server_result.datetime_utc '2024-11-08 15:52:31' _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 4ho8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":301}' # _entry.id 4HO8 # _exptl.entry_id 4HO8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 242.229 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description THYMIDINE _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 90.13 _cell.angle_gamma 90 _cell.entry_id 4HO8 _cell.length_a 71.016 _cell.length_b 91.25 _cell.length_c 91.233 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4HO8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 PISA tetrameric 4 software_defined_assembly 5 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,G,H,I,AA 1 1 B,J,K,L,M,N,O,BA 2 1 C,P,Q,R,S,T,U,CA 3 1 D,V,W,X,Y,Z,DA 4 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA 5 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 ? 3 F N N ? 3 K N N ? 3 Q N N ? 3 W N N # _chem_comp.formula 'C10 H14 N2 O5' _chem_comp.formula_weight 242.229 _chem_comp.id THM _chem_comp.mon_nstd_flag . _chem_comp.name THYMIDINE _chem_comp.type 'dna oh 5 prime terminus' _chem_comp.pdbx_synonyms "DEOXYTHYMIDINE;2'-DEOXYTHYMIDINE" # 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 O5' C5' THM sing 294 n n O5' HO5' THM sing 295 n n C5' C4' THM sing 296 n n C5' "H5'1" THM sing 297 n n C5' "H5'2" THM sing 298 n n C4' O4' THM sing 299 n n C4' C3' THM sing 300 n n C4' H4' THM sing 301 n n O4' C1' THM sing 302 n n C3' O3' THM sing 303 n n C3' C2' THM sing 304 n n C3' H3' THM sing 305 n n O3' HO3' THM sing 306 n n C2' C1' THM sing 307 n n C2' "H2'1" THM sing 308 n n C2' "H2'2" THM sing 309 n n C1' N1 THM sing 310 n n C1' H1' THM sing 311 n n N1 C2 THM sing 312 n n N1 C6 THM sing 313 n n C2 O2 THM doub 314 n n C2 N3 THM sing 315 n n N3 C4 THM sing 316 n n N3 HN3 THM sing 317 n n C4 O4 THM doub 318 n n C4 C5 THM sing 319 n n C5 C5M THM sing 320 n n C5 C6 THM doub 321 n n C5M HM51 THM sing 322 n n C5M HM52 THM sing 323 n n C5M HM53 THM sing 324 n n C6 H6 THM sing 325 n n # _atom_sites.entry_id 4HO8 _atom_sites.fract_transf_matrix[1][1] 0.014081 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000033 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010959 _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] 0.010961 _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 UPG A 1 300 300 UPG UPG . F 3 THM A 1 301 301 THM THM . G 4 SO4 A 1 302 302 SO4 SO4 . H 4 SO4 A 1 303 303 SO4 SO4 . I 4 SO4 A 1 304 304 SO4 SO4 . J 2 UPG B 1 300 300 UPG UPG . K 3 THM B 1 301 301 THM THM . L 4 SO4 B 1 302 302 SO4 SO4 . M 4 SO4 B 1 303 303 SO4 SO4 . N 4 SO4 B 1 304 304 SO4 SO4 . O 4 SO4 B 1 305 305 SO4 SO4 . P 2 UPG C 1 300 300 UPG UPG . Q 3 THM C 1 301 301 THM THM . R 4 SO4 C 1 302 302 SO4 SO4 . S 4 SO4 C 1 303 303 SO4 SO4 . T 4 SO4 C 1 304 304 SO4 SO4 . U 4 SO4 C 1 305 305 SO4 SO4 . V 2 UPG D 1 300 300 UPG UPG . W 3 THM D 1 301 301 THM THM . X 4 SO4 D 1 302 302 SO4 SO4 . Y 4 SO4 D 1 303 303 SO4 SO4 . Z 4 SO4 D 1 304 304 SO4 SO4 . AA 5 HOH A 1 401 4 HOH HOH . AA 5 HOH A 2 402 8 HOH HOH . AA 5 HOH A 3 403 13 HOH HOH . AA 5 HOH A 4 404 18 HOH HOH . AA 5 HOH A 5 405 21 HOH HOH . AA 5 HOH A 6 406 22 HOH HOH . AA 5 HOH A 7 407 23 HOH HOH . AA 5 HOH A 8 408 24 HOH HOH . AA 5 HOH A 9 409 26 HOH HOH . AA 5 HOH A 10 410 31 HOH HOH . AA 5 HOH A 11 411 40 HOH HOH . AA 5 HOH A 12 412 43 HOH HOH . AA 5 HOH A 13 413 45 HOH HOH . AA 5 HOH A 14 414 46 HOH HOH . AA 5 HOH A 15 415 51 HOH HOH . AA 5 HOH A 16 416 56 HOH HOH . AA 5 HOH A 17 417 61 HOH HOH . AA 5 HOH A 18 418 63 HOH HOH . AA 5 HOH A 19 419 65 HOH HOH . AA 5 HOH A 20 420 71 HOH HOH . AA 5 HOH A 21 421 75 HOH HOH . AA 5 HOH A 22 422 76 HOH HOH . AA 5 HOH A 23 423 78 HOH HOH . AA 5 HOH A 24 424 81 HOH HOH . AA 5 HOH A 25 425 86 HOH HOH . AA 5 HOH A 26 426 87 HOH HOH . AA 5 HOH A 27 427 93 HOH HOH . AA 5 HOH A 28 428 94 HOH HOH . AA 5 HOH A 29 429 103 HOH HOH . AA 5 HOH A 30 430 104 HOH HOH . AA 5 HOH A 31 431 107 HOH HOH . AA 5 HOH A 32 432 111 HOH HOH . AA 5 HOH A 33 433 119 HOH HOH . AA 5 HOH A 34 434 124 HOH HOH . AA 5 HOH A 35 435 127 HOH HOH . AA 5 HOH A 36 436 128 HOH HOH . AA 5 HOH A 37 437 130 HOH HOH . AA 5 HOH A 38 438 131 HOH HOH . AA 5 HOH A 39 439 132 HOH HOH . AA 5 HOH A 40 440 134 HOH HOH . AA 5 HOH A 41 441 139 HOH HOH . AA 5 HOH A 42 442 143 HOH HOH . AA 5 HOH A 43 443 153 HOH HOH . AA 5 HOH A 44 444 116 HOH HOH . BA 5 HOH B 1 401 2 HOH HOH . BA 5 HOH B 2 402 3 HOH HOH . BA 5 HOH B 3 403 5 HOH HOH . BA 5 HOH B 4 404 10 HOH HOH . BA 5 HOH B 5 405 14 HOH HOH . BA 5 HOH B 6 406 17 HOH HOH . BA 5 HOH B 7 407 20 HOH HOH . BA 5 HOH B 8 408 28 HOH HOH . BA 5 HOH B 9 409 33 HOH HOH . BA 5 HOH B 10 410 34 HOH HOH . BA 5 HOH B 11 411 38 HOH HOH . BA 5 HOH B 12 412 42 HOH HOH . BA 5 HOH B 13 413 44 HOH HOH . BA 5 HOH B 14 414 50 HOH HOH . BA 5 HOH B 15 415 58 HOH HOH . BA 5 HOH B 16 416 60 HOH HOH . BA 5 HOH B 17 417 62 HOH HOH . BA 5 HOH B 18 418 66 HOH HOH . BA 5 HOH B 19 419 69 HOH HOH . BA 5 HOH B 20 420 73 HOH HOH . BA 5 HOH B 21 421 77 HOH HOH . BA 5 HOH B 22 422 82 HOH HOH . BA 5 HOH B 23 423 84 HOH HOH . BA 5 HOH B 24 424 88 HOH HOH . BA 5 HOH B 25 425 92 HOH HOH . BA 5 HOH B 26 426 96 HOH HOH . BA 5 HOH B 27 427 99 HOH HOH . BA 5 HOH B 28 428 101 HOH HOH . BA 5 HOH B 29 429 102 HOH HOH . BA 5 HOH B 30 430 105 HOH HOH . BA 5 HOH B 31 431 110 HOH HOH . BA 5 HOH B 32 432 112 HOH HOH . BA 5 HOH B 33 433 114 HOH HOH . BA 5 HOH B 34 434 120 HOH HOH . BA 5 HOH B 35 435 135 HOH HOH . BA 5 HOH B 36 436 138 HOH HOH . BA 5 HOH B 37 437 140 HOH HOH . BA 5 HOH B 38 438 142 HOH HOH . BA 5 HOH B 39 439 144 HOH HOH . BA 5 HOH B 40 440 147 HOH HOH . CA 5 HOH C 1 401 1 HOH HOH . CA 5 HOH C 2 402 7 HOH HOH . CA 5 HOH C 3 403 12 HOH HOH . CA 5 HOH C 4 404 27 HOH HOH . CA 5 HOH C 5 405 29 HOH HOH . CA 5 HOH C 6 406 30 HOH HOH . CA 5 HOH C 7 407 35 HOH HOH . CA 5 HOH C 8 408 41 HOH HOH . CA 5 HOH C 9 409 47 HOH HOH . CA 5 HOH C 10 410 52 HOH HOH . CA 5 HOH C 11 411 53 HOH HOH . CA 5 HOH C 12 412 54 HOH HOH . CA 5 HOH C 13 413 57 HOH HOH . CA 5 HOH C 14 414 59 HOH HOH . CA 5 HOH C 15 415 67 HOH HOH . CA 5 HOH C 16 416 68 HOH HOH . CA 5 HOH C 17 417 70 HOH HOH . CA 5 HOH C 18 418 72 HOH HOH . CA 5 HOH C 19 419 80 HOH HOH . CA 5 HOH C 20 420 90 HOH HOH . CA 5 HOH C 21 421 95 HOH HOH . CA 5 HOH C 22 422 106 HOH HOH . CA 5 HOH C 23 423 109 HOH HOH . CA 5 HOH C 24 424 115 HOH HOH . CA 5 HOH C 25 425 117 HOH HOH . CA 5 HOH C 26 426 118 HOH HOH . CA 5 HOH C 27 427 121 HOH HOH . CA 5 HOH C 28 428 123 HOH HOH . CA 5 HOH C 29 429 129 HOH HOH . CA 5 HOH C 30 430 136 HOH HOH . CA 5 HOH C 31 431 137 HOH HOH . CA 5 HOH C 32 432 148 HOH HOH . CA 5 HOH C 33 433 150 HOH HOH . CA 5 HOH C 34 434 151 HOH HOH . CA 5 HOH C 35 435 154 HOH HOH . CA 5 HOH C 36 436 155 HOH HOH . DA 5 HOH D 1 401 6 HOH HOH . DA 5 HOH D 2 402 9 HOH HOH . DA 5 HOH D 3 403 11 HOH HOH . DA 5 HOH D 4 404 15 HOH HOH . DA 5 HOH D 5 405 16 HOH HOH . DA 5 HOH D 6 406 19 HOH HOH . DA 5 HOH D 7 407 25 HOH HOH . DA 5 HOH D 8 408 32 HOH HOH . DA 5 HOH D 9 409 36 HOH HOH . DA 5 HOH D 10 410 37 HOH HOH . DA 5 HOH D 11 411 39 HOH HOH . DA 5 HOH D 12 412 48 HOH HOH . DA 5 HOH D 13 413 49 HOH HOH . DA 5 HOH D 14 414 55 HOH HOH . DA 5 HOH D 15 415 64 HOH HOH . DA 5 HOH D 16 416 74 HOH HOH . DA 5 HOH D 17 417 79 HOH HOH . DA 5 HOH D 18 418 83 HOH HOH . DA 5 HOH D 19 419 85 HOH HOH . DA 5 HOH D 20 420 89 HOH HOH . DA 5 HOH D 21 421 91 HOH HOH . DA 5 HOH D 22 422 97 HOH HOH . DA 5 HOH D 23 423 98 HOH HOH . DA 5 HOH D 24 424 100 HOH HOH . DA 5 HOH D 25 425 108 HOH HOH . DA 5 HOH D 26 426 113 HOH HOH . DA 5 HOH D 27 427 122 HOH HOH . DA 5 HOH D 28 428 125 HOH HOH . DA 5 HOH D 29 429 126 HOH HOH . DA 5 HOH D 30 430 133 HOH HOH . DA 5 HOH D 31 431 141 HOH HOH . DA 5 HOH D 32 432 145 HOH HOH . DA 5 HOH D 33 433 146 HOH HOH . DA 5 HOH D 34 434 149 HOH HOH . DA 5 HOH D 35 435 152 HOH HOH . DA 5 HOH D 36 436 156 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 O5' THM . . . W 3 11.355 -27.854 35.471 1 37.78 ? O5' THM 301 D 1 HETATM 2 C C5' THM . . . W 3 12.229 -26.733 35.223 1 34.08 ? C5' THM 301 D 1 HETATM 3 C C4' THM . . . W 3 11.359 -25.527 34.925 1 34.31 ? C4' THM 301 D 1 HETATM 4 O O4' THM . . . W 3 10.554 -25.794 33.782 1 32.56 ? O4' THM 301 D 1 HETATM 5 C C3' THM . . . W 3 10.4 -25.262 36.07 1 32.46 ? C3' THM 301 D 1 HETATM 6 O O3' THM . . . W 3 10.386 -23.886 36.271 1 31.96 ? O3' THM 301 D 1 HETATM 7 C C2' THM . . . W 3 9.033 -25.657 35.601 1 31.25 ? C2' THM 301 D 1 HETATM 8 C C1' THM . . . W 3 9.167 -25.61 34.1 1 32.49 ? C1' THM 301 D 1 HETATM 9 N N1 THM . . . W 3 8.436 -26.639 33.386 1 33.26 ? N1 THM 301 D 1 HETATM 10 C C2 THM . . . W 3 7.651 -26.27 32.364 1 36.5 ? C2 THM 301 D 1 HETATM 11 O O2 THM . . . W 3 7.491 -25.047 32.097 1 35.73 ? O2 THM 301 D 1 HETATM 12 N N3 THM . . . W 3 7.022 -27.193 31.615 1 39.59 ? N3 THM 301 D 1 HETATM 13 C C4 THM . . . W 3 7.181 -28.5 31.859 1 39.65 ? C4 THM 301 D 1 HETATM 14 O O4 THM . . . W 3 6.56 -29.329 31.143 1 42.81 ? O4 THM 301 D 1 HETATM 15 C C5 THM . . . W 3 8.012 -28.903 32.912 1 38.25 ? C5 THM 301 D 1 HETATM 16 C C5M THM . . . W 3 8.237 -30.362 33.257 1 34.21 ? C5M THM 301 D 1 HETATM 17 C C6 THM . . . W 3 8.646 -27.923 33.662 1 35.79 ? C6 THM 301 D 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 230 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 17 #