data_1G3L # _model_server_result.job_id xqJ9obS9U_gpBzn2ZO2hUg _model_server_result.datetime_utc '2024-10-12 10:14:45' _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 1g3l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":504}' # _entry.id 1G3L # _exptl.entry_id 1G3L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 548.33 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE" _entity.pdbx_number_of_molecules 8 _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 1G3L _cell.length_a 71.087 _cell.length_b 138.557 _cell.length_c 139.676 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1G3L _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 G N N ? 3 J N N ? 3 K N N ? 3 M N N ? 3 N N N ? 3 P N N ? 3 Q 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 1G3L _atom_sites.fract_transf_matrix[1][1] 0.014067 _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] 0.007217 _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] 0.007159 _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 SO4 A 1 701 701 SO4 SO4 . F 3 TRH A 1 500 500 TRH TDR . G 3 TRH A 1 501 600 TRH TDR . H 2 SO4 B 1 700 700 SO4 SO4 . I 2 SO4 B 1 702 702 SO4 SO4 . J 3 TRH B 1 502 500 TRH TDR . K 3 TRH B 1 503 600 TRH TDR . L 2 SO4 C 1 703 703 SO4 SO4 . M 3 TRH C 1 504 500 TRH TDR . N 3 TRH C 1 505 600 TRH TDR . O 2 SO4 D 1 704 704 SO4 SO4 . P 3 TRH D 1 506 500 TRH TDR . Q 3 TRH D 1 507 600 TRH TDR . # 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 . . . M 3 10.498 47.62 12.94 1 9.8 ? O4P TRH 504 C 1 HETATM 2 P P2 TRH . . . M 3 10.494 48.447 14.327 1 13.12 ? P2 TRH 504 C 1 HETATM 3 O O3P TRH . . . M 3 11.892 48.86 14.993 1 10.35 ? O3P TRH 504 C 1 HETATM 4 O O1 TRH . . . M 3 9.71 49.786 14.183 1 11.57 ? O1 TRH 504 C 1 HETATM 5 C C1 TRH . . . M 3 8.934 49.955 13.023 1 13.55 ? C1 TRH 504 C 1 HETATM 6 C C2 TRH . . . M 3 9.667 50.222 11.723 1 13.79 ? C2 TRH 504 C 1 HETATM 7 O O2 TRH . . . M 3 10.389 51.424 11.872 1 12.5 ? O2 TRH 504 C 1 HETATM 8 C C3 TRH . . . M 3 8.604 50.444 10.668 1 13.95 ? C3 TRH 504 C 1 HETATM 9 O O3 TRH . . . M 3 9.064 51.05 9.466 1 17.29 ? O3 TRH 504 C 1 HETATM 10 C C4 TRH . . . M 3 7.645 51.423 11.265 1 13.73 ? C4 TRH 504 C 1 HETATM 11 O O4 TRH . . . M 3 6.487 51.587 10.414 1 13.21 ? O4 TRH 504 C 1 HETATM 12 C C5 TRH . . . M 3 7.242 50.923 12.637 1 12.77 ? C5 TRH 504 C 1 HETATM 13 O O5 TRH . . . M 3 8.307 51.033 13.598 1 15.29 ? O5 TRH 504 C 1 HETATM 14 C C6 TRH . . . M 3 5.964 51.639 12.986 1 14.02 ? C6 TRH 504 C 1 HETATM 15 O OPP TRH . . . M 3 9.544 47.739 15.397 1 12.98 ? OPP TRH 504 C 1 HETATM 16 P P TRH . . . M 3 9.788 47.992 16.99 1 13.42 ? P TRH 504 C 1 HETATM 17 O O1P TRH . . . M 3 9.274 49.449 17.385 1 12.55 ? O1P TRH 504 C 1 HETATM 18 O O2P TRH . . . M 3 11.224 47.496 17.502 1 11.26 ? O2P TRH 504 C 1 HETATM 19 O O5' TRH . . . M 3 8.679 46.997 17.523 1 12.2 ? O5' TRH 504 C 1 HETATM 20 C C5' TRH . . . M 3 7.429 47.599 17.38 1 11.83 ? C5' TRH 504 C 1 HETATM 21 C C4' TRH . . . M 3 6.411 47.093 18.362 1 14.67 ? C4' TRH 504 C 1 HETATM 22 O O4' TRH . . . M 3 5.849 45.952 17.803 1 15.76 ? O4' TRH 504 C 1 HETATM 23 C C3' TRH . . . M 3 6.781 46.497 19.669 1 14.18 ? C3' TRH 504 C 1 HETATM 24 O O3' TRH . . . M 3 5.59 46.67 20.44 1 12.77 ? O3' TRH 504 C 1 HETATM 25 C C2' TRH . . . M 3 6.885 45.026 19.485 1 13.4 ? C2' TRH 504 C 1 HETATM 26 C C1' TRH . . . M 3 6.148 44.613 18.249 1 14.77 ? C1' TRH 504 C 1 HETATM 27 N N11 TRH . . . M 3 6.939 43.623 17.451 1 16.34 ? N11 TRH 504 C 1 HETATM 28 C C21 TRH . . . M 3 6.404 42.398 17.328 1 13.81 ? C21 TRH 504 C 1 HETATM 29 O O21 TRH . . . M 3 5.248 42.215 17.929 1 10.5 ? O21 TRH 504 C 1 HETATM 30 N N31 TRH . . . M 3 6.992 41.405 16.634 1 15.03 ? N31 TRH 504 C 1 HETATM 31 C C41 TRH . . . M 3 8.151 41.599 16.023 1 18.77 ? C41 TRH 504 C 1 HETATM 32 O O41 TRH . . . M 3 8.715 40.604 15.331 1 21.03 ? O41 TRH 504 C 1 HETATM 33 C C51 TRH . . . M 3 8.751 42.854 16.1 1 18.89 ? C51 TRH 504 C 1 HETATM 34 C C5A TRH . . . M 3 10.075 43.088 15.412 1 17.85 ? C5A TRH 504 C 1 HETATM 35 C C61 TRH . . . M 3 8.127 43.874 16.833 1 17.45 ? C61 TRH 504 C 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 35 #