data_2P1D # _model_server_result.job_id hYahv_O_MechICgDpHK9MA _model_server_result.datetime_utc '2024-11-05 12:46:17' _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 2p1d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":911}' # _entry.id 2P1D # _exptl.entry_id 2P1D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _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 2P1D _cell.length_a 112.198 _cell.length_b 112.198 _cell.length_c 56.462 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2P1D _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 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 PQS monomeric 1 author_and_software_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,D,E,F,G,H,I,J,K,L,M,N 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N 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' 6_555 -x,-x+y,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 18.820667 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id L _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag n _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _chem_comp.type 'l-peptide linking' _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 N CA SAH sing 317 n n N HN1 SAH sing 318 n n N HN2 SAH sing 319 n n CA CB SAH sing 320 n n CA C SAH sing 321 n n CA HA SAH sing 322 n n CB CG SAH sing 323 n n CB HB1 SAH sing 324 n n CB HB2 SAH sing 325 n n CG SD SAH sing 326 n n CG HG1 SAH sing 327 n n CG HG2 SAH sing 328 n n SD C5' SAH sing 329 n n C O SAH doub 330 n n C OXT SAH sing 331 n n OXT HXT SAH sing 332 n n C5' C4' SAH sing 333 n n C5' "H5'1" SAH sing 334 n n C5' "H5'2" SAH sing 335 n n C4' O4' SAH sing 336 n n C4' C3' SAH sing 337 n n C4' H4' SAH sing 338 n n O4' C1' SAH sing 339 n n C3' O3' SAH sing 340 n n C3' C2' SAH sing 341 n n C3' H3' SAH sing 342 n n O3' HO3' SAH sing 343 n n C2' O2' SAH sing 344 n n C2' C1' SAH sing 345 n n C2' H2' SAH sing 346 n n O2' HO2' SAH sing 347 n n C1' N9 SAH sing 348 n n C1' H1' SAH sing 349 n n N9 C8 SAH sing 350 n y N9 C4 SAH sing 351 n y C8 N7 SAH doub 352 n y C8 H8 SAH sing 353 n n N7 C5 SAH sing 354 n y C5 C6 SAH sing 355 n y C5 C4 SAH doub 356 n y C6 N6 SAH sing 357 n n C6 N1 SAH doub 358 n y N6 HN61 SAH sing 359 n n N6 HN62 SAH sing 360 n n N1 C2 SAH sing 361 n y C2 N3 SAH doub 362 n y C2 H2 SAH sing 363 n n N3 C4 SAH sing 364 n y # _atom_sites.entry_id 2P1D _atom_sites.fract_transf_matrix[1][1] 0.008913 _atom_sites.fract_transf_matrix[1][2] 0.005146 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010292 _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] 0.017711 _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 SO4 A 1 901 901 SO4 SO4 . C 2 SO4 A 1 902 902 SO4 SO4 . D 2 SO4 A 1 903 903 SO4 SO4 . E 2 SO4 A 1 904 904 SO4 SO4 . F 2 SO4 A 1 905 905 SO4 SO4 . G 2 SO4 A 1 906 906 SO4 SO4 . H 2 SO4 A 1 907 907 SO4 SO4 . I 2 SO4 A 1 908 908 SO4 SO4 . J 2 SO4 A 1 909 909 SO4 SO4 . K 2 SO4 A 1 910 910 SO4 SO4 . L 3 SAH A 1 911 911 SAH SAH . M 4 5GP A 1 912 912 5GP 5GP . N 5 HOH A 1 913 1 HOH HOH . N 5 HOH A 2 914 2 HOH HOH . N 5 HOH A 3 915 3 HOH HOH . N 5 HOH A 4 916 5 HOH HOH . N 5 HOH A 5 917 6 HOH HOH . N 5 HOH A 6 918 7 HOH HOH . N 5 HOH A 7 919 8 HOH HOH . N 5 HOH A 8 920 9 HOH HOH . N 5 HOH A 9 921 11 HOH HOH . N 5 HOH A 10 922 12 HOH HOH . N 5 HOH A 11 923 13 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 N SAH . . . L 3 10.287 -45.983 -1.395 1 61.76 ? N SAH 911 A 1 HETATM 2 C CA SAH . . . L 3 11.527 -46.757 -1.378 1 62.1 ? CA SAH 911 A 1 HETATM 3 C CB SAH . . . L 3 12.114 -46.836 0.038 1 64.05 ? CB SAH 911 A 1 HETATM 4 C CG SAH . . . L 3 13.172 -45.876 0.249 1 69.18 ? CG SAH 911 A 1 HETATM 5 S SD SAH . . . L 3 13.937 -45.898 1.91 1 75.27 ? SD SAH 911 A 1 HETATM 6 C C SAH . . . L 3 11.329 -48.181 -1.961 1 61.61 ? C SAH 911 A 1 HETATM 7 O O SAH . . . L 3 10.168 -48.421 -2.362 1 60.83 ? O SAH 911 A 1 HETATM 8 O OXT SAH . . . L 3 12.219 -48.459 -2.821 1 59.99 ? OXT SAH 911 A 1 HETATM 9 C C5' SAH . . . L 3 14.285 -44.143 2.068 1 74.8 ? C5' SAH 911 A 1 HETATM 10 C C4' SAH . . . L 3 15.393 -43.574 1.198 1 75.09 ? C4' SAH 911 A 1 HETATM 11 O O4' SAH . . . L 3 15.517 -42.172 1.477 1 75.83 ? O4' SAH 911 A 1 HETATM 12 C C3' SAH . . . L 3 16.782 -44.142 1.468 1 74.47 ? C3' SAH 911 A 1 HETATM 13 O O3' SAH . . . L 3 17.099 -45.042 0.401 1 72.99 ? O3' SAH 911 A 1 HETATM 14 C C2' SAH . . . L 3 17.754 -42.946 1.511 1 74.4 ? C2' SAH 911 A 1 HETATM 15 O O2' SAH . . . L 3 18.918 -43.013 0.699 1 76.77 ? O2' SAH 911 A 1 HETATM 16 C C1' SAH . . . L 3 16.828 -41.773 1.207 1 75.47 ? C1' SAH 911 A 1 HETATM 17 N N9 SAH . . . L 3 17.105 -40.528 1.94 1 75.58 ? N9 SAH 911 A 1 HETATM 18 C C8 SAH . . . L 3 17.268 -40.334 3.291 1 75.89 ? C8 SAH 911 A 1 HETATM 19 N N7 SAH . . . L 3 17.499 -39.085 3.624 1 75.99 ? N7 SAH 911 A 1 HETATM 20 C C5 SAH . . . L 3 17.488 -38.401 2.411 1 75.45 ? C5 SAH 911 A 1 HETATM 21 C C6 SAH . . . L 3 17.671 -37.021 2.06 1 75.37 ? C6 SAH 911 A 1 HETATM 22 N N6 SAH . . . L 3 17.906 -36.067 2.962 1 74.82 ? N6 SAH 911 A 1 HETATM 23 N N1 SAH . . . L 3 17.598 -36.671 0.721 1 74.03 ? N1 SAH 911 A 1 HETATM 24 C C2 SAH . . . L 3 17.36 -37.643 -0.159 1 73.46 ? C2 SAH 911 A 1 HETATM 25 N N3 SAH . . . L 3 17.169 -38.97 0.051 1 74.5 ? N3 SAH 911 A 1 HETATM 26 C C4 SAH . . . L 3 17.245 -39.289 1.35 1 75.44 ? C4 SAH 911 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 26 #