data_4ESH # _model_server_result.job_id pcg9ALTTfwefcAYuUc1z6A _model_server_result.datetime_utc '2024-11-29 14:12:39' _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 4esh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4ESH # _exptl.entry_id 4ESH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 242.229 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description THYMIDINE _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 4ESH _cell.length_a 55.352 _cell.length_b 55.352 _cell.length_c 114.767 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ESH _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 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 ? monomeric 1 author_defined_assembly 1 PISA dimeric 2 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 1 1 A,B,C 2 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' 5_555 x-y,-y,-z+1/3 1 0 0 0 -1 0 0 0 -1 0 0 38.255667 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 290 n n O5' HO5' THM sing 291 n n C5' C4' THM sing 292 n n C5' "H5'1" THM sing 293 n n C5' "H5'2" THM sing 294 n n C4' O4' THM sing 295 n n C4' C3' THM sing 296 n n C4' H4' THM sing 297 n n O4' C1' THM sing 298 n n C3' O3' THM sing 299 n n C3' C2' THM sing 300 n n C3' H3' THM sing 301 n n O3' HO3' THM sing 302 n n C2' C1' THM sing 303 n n C2' "H2'1" THM sing 304 n n C2' "H2'2" THM sing 305 n n C1' N1 THM sing 306 n n C1' H1' THM sing 307 n n N1 C2 THM sing 308 n n N1 C6 THM sing 309 n n C2 O2 THM doub 310 n n C2 N3 THM sing 311 n n N3 C4 THM sing 312 n n N3 HN3 THM sing 313 n n C4 O4 THM doub 314 n n C4 C5 THM sing 315 n n C5 C5M THM sing 316 n n C5 C6 THM doub 317 n n C5M HM51 THM sing 318 n n C5M HM52 THM sing 319 n n C5M HM53 THM sing 320 n n C6 H6 THM sing 321 n n # _atom_sites.entry_id 4ESH _atom_sites.fract_transf_matrix[1][1] 0.018066 _atom_sites.fract_transf_matrix[1][2] 0.010431 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020861 _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] 0.008713 _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 THM A 1 301 1 THM THM . C 3 HOH A 1 401 1 HOH HOH . C 3 HOH A 2 402 2 HOH HOH . C 3 HOH A 3 403 3 HOH HOH . C 3 HOH A 4 404 4 HOH HOH . C 3 HOH A 5 405 5 HOH HOH . C 3 HOH A 6 406 6 HOH HOH . C 3 HOH A 7 407 7 HOH HOH . C 3 HOH A 8 408 8 HOH HOH . C 3 HOH A 9 409 9 HOH HOH . C 3 HOH A 10 410 10 HOH HOH . C 3 HOH A 11 411 11 HOH HOH . C 3 HOH A 12 412 12 HOH HOH . C 3 HOH A 13 413 13 HOH HOH . C 3 HOH A 14 414 14 HOH HOH . C 3 HOH A 15 415 15 HOH HOH . C 3 HOH A 16 416 16 HOH HOH . C 3 HOH A 17 417 17 HOH HOH . C 3 HOH A 18 418 18 HOH HOH . C 3 HOH A 19 419 19 HOH HOH . C 3 HOH A 20 420 20 HOH HOH . C 3 HOH A 21 421 21 HOH HOH . C 3 HOH A 22 422 22 HOH HOH . C 3 HOH A 23 423 23 HOH HOH . C 3 HOH A 24 424 24 HOH HOH . C 3 HOH A 25 425 25 HOH HOH . C 3 HOH A 26 426 26 HOH HOH . C 3 HOH A 27 427 27 HOH HOH . C 3 HOH A 28 428 28 HOH HOH . C 3 HOH A 29 429 29 HOH HOH . C 3 HOH A 30 430 30 HOH HOH . C 3 HOH A 31 431 31 HOH HOH . C 3 HOH A 32 432 32 HOH HOH . C 3 HOH A 33 433 33 HOH HOH . C 3 HOH A 34 434 34 HOH HOH . C 3 HOH A 35 435 35 HOH HOH . C 3 HOH A 36 436 36 HOH HOH . C 3 HOH A 37 437 37 HOH HOH . C 3 HOH A 38 438 38 HOH HOH . C 3 HOH A 39 439 39 HOH HOH . C 3 HOH A 40 440 40 HOH HOH . C 3 HOH A 41 441 41 HOH HOH . C 3 HOH A 42 442 42 HOH HOH . C 3 HOH A 43 443 43 HOH HOH . C 3 HOH A 44 444 44 HOH HOH . C 3 HOH A 45 445 45 HOH HOH . C 3 HOH A 46 446 46 HOH HOH . C 3 HOH A 47 447 47 HOH HOH . C 3 HOH A 48 448 48 HOH HOH . C 3 HOH A 49 449 49 HOH HOH . C 3 HOH A 50 450 50 HOH HOH . C 3 HOH A 51 451 51 HOH HOH . C 3 HOH A 52 452 52 HOH HOH . C 3 HOH A 53 453 53 HOH HOH . C 3 HOH A 54 454 54 HOH HOH . C 3 HOH A 55 455 55 HOH HOH . C 3 HOH A 56 456 56 HOH HOH . C 3 HOH A 57 457 57 HOH HOH . C 3 HOH A 58 458 58 HOH HOH . C 3 HOH A 59 459 59 HOH HOH . C 3 HOH A 60 460 60 HOH HOH . C 3 HOH A 61 461 61 HOH HOH . C 3 HOH A 62 462 62 HOH HOH . C 3 HOH A 63 463 63 HOH HOH . C 3 HOH A 64 464 64 HOH HOH . C 3 HOH A 65 465 65 HOH HOH . C 3 HOH A 66 466 66 HOH HOH . C 3 HOH A 67 467 67 HOH HOH . C 3 HOH A 68 468 68 HOH HOH . C 3 HOH A 69 469 69 HOH HOH . C 3 HOH A 70 470 70 HOH HOH . C 3 HOH A 71 471 71 HOH HOH . C 3 HOH A 72 472 72 HOH HOH . C 3 HOH A 73 473 73 HOH HOH . C 3 HOH A 74 474 74 HOH HOH . C 3 HOH A 75 475 75 HOH HOH . C 3 HOH A 76 476 76 HOH HOH . C 3 HOH A 77 477 77 HOH HOH . C 3 HOH A 78 478 78 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 . . . B 2 -18.776 13.042 11.77 1 38.83 ? O5' THM 301 A 1 HETATM 2 C C5' THM . . . B 2 -17.935 12.029 11.352 1 27.42 ? C5' THM 301 A 1 HETATM 3 C C4' THM . . . B 2 -18.521 11.268 10.192 1 34.68 ? C4' THM 301 A 1 HETATM 4 O O4' THM . . . B 2 -19.584 10.444 10.568 1 34.05 ? O4' THM 301 A 1 HETATM 5 C C3' THM . . . B 2 -18.994 12.143 9.088 1 34.36 ? C3' THM 301 A 1 HETATM 6 O O3' THM . . . B 2 -18.594 11.575 7.9 1 33.83 ? O3' THM 301 A 1 HETATM 7 C C2' THM . . . B 2 -20.471 12.115 9.182 1 33.44 ? C2' THM 301 A 1 HETATM 8 C C1' THM . . . B 2 -20.691 10.757 9.757 1 36.11 ? C1' THM 301 A 1 HETATM 9 N N1 THM . . . B 2 -21.867 10.648 10.581 1 32.06 ? N1 THM 301 A 1 HETATM 10 C C2 THM . . . B 2 -22.915 9.711 10.272 1 28.97 ? C2 THM 301 A 1 HETATM 11 O O2 THM . . . B 2 -22.874 9.005 9.274 1 29.92 ? O2 THM 301 A 1 HETATM 12 N N3 THM . . . B 2 -24.04 9.612 11.126 1 25.63 ? N3 THM 301 A 1 HETATM 13 C C4 THM . . . B 2 -24.135 10.38 12.301 1 25.53 ? C4 THM 301 A 1 HETATM 14 O O4 THM . . . B 2 -25.116 10.259 13.027 1 29.52 ? O4 THM 301 A 1 HETATM 15 C C5 THM . . . B 2 -23.054 11.335 12.635 1 28.39 ? C5 THM 301 A 1 HETATM 16 C C5M THM . . . B 2 -23.138 12.168 13.873 1 25.39 ? C5M THM 301 A 1 HETATM 17 C C6 THM . . . B 2 -21.961 11.44 11.796 1 32.7 ? C6 THM 301 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 452 _model_server_stats.encode_time_ms 34 _model_server_stats.element_count 17 #