data_7VCH # _model_server_result.job_id hANLovjHLvuOioaBCJ2FXQ _model_server_result.datetime_utc '2024-10-10 11:16:16' _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 7vch # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 7VCH # _exptl.entry_id 7VCH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 548.33 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE" _entity.pdbx_number_of_molecules 2 _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 7VCH _cell.length_a 47.407 _cell.length_b 124.402 _cell.length_c 127.647 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7VCH _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F 1 1 B,G,H,I 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 C N N ? 2 G N N # _chem_comp.formula 'C16 H26 N2 O15 P2' _chem_comp.formula_weight 548.33 _chem_comp.id TRH _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE" _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 O4P P2 TRH sing 308 n n O4P H4PO TRH sing 309 n n P2 O3P TRH doub 310 n n P2 O1 TRH sing 311 n n P2 OPP TRH sing 312 n n O1 C1 TRH sing 313 n n C1 C2 TRH sing 314 n n C1 O5 TRH sing 315 n n C1 HC1 TRH sing 316 n n C2 O2 TRH sing 317 n n C2 C3 TRH sing 318 n n C2 HC2 TRH sing 319 n n O2 HO2 TRH sing 320 n n C3 O3 TRH sing 321 n n C3 C4 TRH sing 322 n n C3 HC3 TRH sing 323 n n O3 HO3 TRH sing 324 n n C4 O4 TRH sing 325 n n C4 C5 TRH sing 326 n n C4 HC4 TRH sing 327 n n O4 HO4 TRH sing 328 n n C5 O5 TRH sing 329 n n C5 C6 TRH sing 330 n n C5 HC5 TRH sing 331 n n C6 HC61 TRH sing 332 n n C6 HC62 TRH sing 333 n n C6 HC63 TRH sing 334 n n OPP P TRH sing 335 n n P O1P TRH sing 336 n n P O2P TRH doub 337 n n P O5' TRH sing 338 n n O1P H1PO TRH sing 339 n n O5' C5' TRH sing 340 n n C5' C4' TRH sing 341 n n C5' "H5'1" TRH sing 342 n n C5' "H5'2" TRH sing 343 n n C4' O4' TRH sing 344 n n C4' C3' TRH sing 345 n n C4' "H4'C" TRH sing 346 n n O4' C1' TRH sing 347 n n C3' O3' TRH sing 348 n n C3' C2' TRH sing 349 n n C3' "H3'C" TRH sing 350 n n O3' "H3'O" TRH sing 351 n n C2' C1' TRH sing 352 n n C2' "H2'1" TRH sing 353 n n C2' "H2'2" TRH sing 354 n n C1' N11 TRH sing 355 n n C1' "H1'C" TRH sing 356 n n N11 C21 TRH sing 357 n n N11 C61 TRH sing 358 n n C21 O21 TRH doub 359 n n C21 N31 TRH sing 360 n n N31 C41 TRH sing 361 n n N31 H31N TRH sing 362 n n C41 O41 TRH doub 363 n n C41 C51 TRH sing 364 n n C51 C5A TRH sing 365 n n C51 C61 TRH doub 366 n n C5A HCA1 TRH sing 367 n n C5A HCA2 TRH sing 368 n n C5A HCA3 TRH sing 369 n n C61 H61C TRH sing 370 n n # _atom_sites.entry_id 7VCH _atom_sites.fract_transf_matrix[1][1] 0.021094 _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] 0.008038 _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] 0.007834 _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 C 2 TRH A 1 401 401 TRH TRH . D 3 SO4 A 1 402 1 SO4 SO4 . E 3 SO4 A 1 403 2 SO4 SO4 . F 3 SO4 A 1 404 3 SO4 SO4 . G 2 TRH F 1 401 401 TRH TRH . H 3 SO4 F 1 402 4 SO4 SO4 . I 3 SO4 F 1 403 5 SO4 SO4 . # 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 O4P TRH . . . C 2 32.341 -13.589 -13.7 1 65.87 ? O4P TRH 401 A 1 HETATM 2 P P2 TRH . . . C 2 31.496 -14.12 -12.599 1 65.03 ? P2 TRH 401 A 1 HETATM 3 O O3P TRH . . . C 2 32.16 -15.001 -11.608 1 57.93 ? O3P TRH 401 A 1 HETATM 4 O O1 TRH . . . C 2 30.818 -12.893 -11.845 1 60.96 ? O1 TRH 401 A 1 HETATM 5 C C1 TRH . . . C 2 30.202 -12.968 -10.594 1 60.05 ? C1 TRH 401 A 1 HETATM 6 C C2 TRH . . . C 2 29.256 -11.798 -10.507 1 70.34 ? C2 TRH 401 A 1 HETATM 7 O O2 TRH . . . C 2 30 -10.599 -10.683 1 74.45 ? O2 TRH 401 A 1 HETATM 8 C C3 TRH . . . C 2 28.613 -11.762 -9.159 1 67.77 ? C3 TRH 401 A 1 HETATM 9 O O3 TRH . . . C 2 27.766 -10.623 -9.1 1 70.12 ? O3 TRH 401 A 1 HETATM 10 C C4 TRH . . . C 2 29.683 -11.655 -8.103 1 64.36 ? C4 TRH 401 A 1 HETATM 11 O O4 TRH . . . C 2 29.088 -11.658 -6.815 1 70.51 ? O4 TRH 401 A 1 HETATM 12 C C5 TRH . . . C 2 30.639 -12.829 -8.244 1 72.17 ? C5 TRH 401 A 1 HETATM 13 O O5 TRH . . . C 2 31.183 -12.853 -9.582 1 69.31 ? O5 TRH 401 A 1 HETATM 14 C C6 TRH . . . C 2 31.819 -12.743 -7.307 1 72.13 ? C6 TRH 401 A 1 HETATM 15 O OPP TRH . . . C 2 30.243 -14.884 -13.231 1 60.42 ? OPP TRH 401 A 1 HETATM 16 P P TRH . . . C 2 28.903 -14.489 -14.007 1 57.87 ? P TRH 401 A 1 HETATM 17 O O1P TRH . . . C 2 28.333 -15.719 -14.606 1 49.35 ? O1P TRH 401 A 1 HETATM 18 O O2P TRH . . . C 2 28.021 -13.702 -13.108 1 57.3 ? O2P TRH 401 A 1 HETATM 19 O O5' TRH . . . C 2 29.45 -13.547 -15.166 1 48.89 ? O5' TRH 401 A 1 HETATM 20 C C5' TRH . . . C 2 30.353 -14.085 -16.147 1 52.64 ? C5' TRH 401 A 1 HETATM 21 C C4' TRH . . . C 2 30.037 -13.457 -17.477 1 49.33 ? C4' TRH 401 A 1 HETATM 22 O O4' TRH . . . C 2 31.048 -13.832 -18.436 1 52.03 ? O4' TRH 401 A 1 HETATM 23 C C3' TRH . . . C 2 28.709 -13.909 -18.075 1 52.4 ? C3' TRH 401 A 1 HETATM 24 O O3' TRH . . . C 2 28.165 -12.818 -18.806 1 51.15 ? O3' TRH 401 A 1 HETATM 25 C C2' TRH . . . C 2 29.147 -14.987 -19.052 1 50.31 ? C2' TRH 401 A 1 HETATM 26 C C1' TRH . . . C 2 30.407 -14.348 -19.59 1 54.03 ? C1' TRH 401 A 1 HETATM 27 N N11 TRH . . . C 2 31.348 -15.266 -20.245 1 59.47 ? N11 TRH 401 A 1 HETATM 28 C C21 TRH . . . C 2 31.729 -14.98 -21.535 1 63.89 ? C21 TRH 401 A 1 HETATM 29 O O21 TRH . . . C 2 31.31 -14.012 -22.149 1 61.85 ? O21 TRH 401 A 1 HETATM 30 N N31 TRH . . . C 2 32.62 -15.865 -22.081 1 67.97 ? N31 TRH 401 A 1 HETATM 31 C C41 TRH . . . C 2 33.156 -16.983 -21.48 1 63.26 ? C41 TRH 401 A 1 HETATM 32 O O41 TRH . . . C 2 33.949 -17.691 -22.096 1 69.51 ? O41 TRH 401 A 1 HETATM 33 C C51 TRH . . . C 2 32.717 -17.221 -20.128 1 60.94 ? C51 TRH 401 A 1 HETATM 34 C C5A TRH . . . C 2 33.256 -18.421 -19.416 1 63.64 ? C5A TRH 401 A 1 HETATM 35 C C61 TRH . . . C 2 31.848 -16.362 -19.576 1 59.02 ? C61 TRH 401 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 35 #