data_2VDW # _model_server_result.job_id gWgxdSRApXW3LSH2cp0egw _model_server_result.datetime_utc '2025-02-05 07:42:03' _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 2vdw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1846}' # _entry.id 2VDW # _exptl.entry_id 2VDW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 94.22 _cell.angle_beta 92.95 _cell.angle_gamma 108.26 _cell.entry_id 2VDW _cell.length_a 60.89 _cell.length_b 61.02 _cell.length_c 225.78 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VDW _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 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 dimeric 2 software_defined_assembly 1 PQS dimeric 2 author_and_software_defined_assembly 2 PQS dimeric 2 author_and_software_defined_assembly 3 PQS dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,I,J 1 1 C,D,K,L,M 2 1 E,F,N,O,P,Q 3 1 G,H,R,S,T,U,V,W 4 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 ? 4 J N N ? 4 L N N ? 4 O N N ? 4 S N 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 275 n n N HN1 SAH sing 276 n n N HN2 SAH sing 277 n n CA CB SAH sing 278 n n CA C SAH sing 279 n n CA HA SAH sing 280 n n CB CG SAH sing 281 n n CB HB1 SAH sing 282 n n CB HB2 SAH sing 283 n n CG SD SAH sing 284 n n CG HG1 SAH sing 285 n n CG HG2 SAH sing 286 n n SD C5' SAH sing 287 n n C O SAH doub 288 n n C OXT SAH sing 289 n n OXT HXT SAH sing 290 n n C5' C4' SAH sing 291 n n C5' "H5'1" SAH sing 292 n n C5' "H5'2" SAH sing 293 n n C4' O4' SAH sing 294 n n C4' C3' SAH sing 295 n n C4' H4' SAH sing 296 n n O4' C1' SAH sing 297 n n C3' O3' SAH sing 298 n n C3' C2' SAH sing 299 n n C3' H3' SAH sing 300 n n O3' HO3' SAH sing 301 n n C2' O2' SAH sing 302 n n C2' C1' SAH sing 303 n n C2' H2' SAH sing 304 n n O2' HO2' SAH sing 305 n n C1' N9 SAH sing 306 n n C1' H1' SAH sing 307 n n N9 C8 SAH sing 308 n y N9 C4 SAH sing 309 n y C8 N7 SAH doub 310 n y C8 H8 SAH sing 311 n n N7 C5 SAH sing 312 n y C5 C6 SAH sing 313 n y C5 C4 SAH doub 314 n y C6 N6 SAH sing 315 n n C6 N1 SAH doub 316 n y N6 HN61 SAH sing 317 n n N6 HN62 SAH sing 318 n n N1 C2 SAH sing 319 n y C2 N3 SAH doub 320 n y C2 H2 SAH sing 321 n n N3 C4 SAH sing 322 n y # _atom_sites.entry_id 2VDW _atom_sites.fract_transf_matrix[1][1] 0.016423 _atom_sites.fract_transf_matrix[1][2] 0.005419 _atom_sites.fract_transf_matrix[1][3] 0.001365 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017257 _atom_sites.fract_transf_matrix[2][3] 0.00164 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.004455 _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 I 3 SO4 A 1 1845 1845 SO4 SO4 . J 4 SAH A 1 1846 1846 SAH SAH . K 3 SO4 C 1 1845 1845 SO4 SO4 . L 4 SAH C 1 1846 1846 SAH SAH . M 3 SO4 C 1 1847 1847 SO4 SO4 . N 3 SO4 E 1 1845 1845 SO4 SO4 . O 4 SAH E 1 1846 1846 SAH SAH . P 3 SO4 F 1 1288 1288 SO4 SO4 . Q 3 SO4 F 1 1289 1289 SO4 SO4 . R 3 SO4 G 1 1845 1845 SO4 SO4 . S 4 SAH G 1 1846 1846 SAH SAH . T 3 SO4 H 1 1288 1288 SO4 SO4 . U 3 SO4 H 1 1289 1289 SO4 SO4 . V 3 SO4 H 1 1290 1290 SO4 SO4 . W 3 SO4 H 1 1291 1291 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 N N SAH . . . J 4 3.486 -15.065 12.114 1 19.67 ? N SAH 1846 A 1 HETATM 2 C CA SAH . . . J 4 2.418 -15.368 13.108 1 20.23 ? CA SAH 1846 A 1 HETATM 3 C CB SAH . . . J 4 2.964 -15.681 14.515 1 20.67 ? CB SAH 1846 A 1 HETATM 4 C CG SAH . . . J 4 3.762 -14.6 15.25 1 20.57 ? CG SAH 1846 A 1 HETATM 5 S SD SAH . . . J 4 3.922 -15.043 16.994 1 21.96 ? SD SAH 1846 A 1 HETATM 6 C C SAH . . . J 4 1.404 -14.229 13.205 1 20.32 ? C SAH 1846 A 1 HETATM 7 O O SAH . . . J 4 1.723 -13.091 12.8 1 19.77 ? O SAH 1846 A 1 HETATM 8 O OXT SAH . . . J 4 0.267 -14.449 13.694 1 19.92 ? OXT SAH 1846 A 1 HETATM 9 C C5' SAH . . . J 4 5.701 -15.402 17.048 1 19.41 ? C5' SAH 1846 A 1 HETATM 10 C C4' SAH . . . J 4 6.055 -16.765 16.462 1 19.65 ? C4' SAH 1846 A 1 HETATM 11 O O4' SAH . . . J 4 7.457 -16.897 16.415 1 18.7 ? O4' SAH 1846 A 1 HETATM 12 C C3' SAH . . . J 4 5.541 -17.961 17.25 1 19.66 ? C3' SAH 1846 A 1 HETATM 13 O O3' SAH . . . J 4 4.745 -18.731 16.387 1 19.63 ? O3' SAH 1846 A 1 HETATM 14 C C2' SAH . . . J 4 6.798 -18.68 17.725 1 20.55 ? C2' SAH 1846 A 1 HETATM 15 O O2' SAH . . . J 4 6.786 -20.095 17.749 1 22.38 ? O2' SAH 1846 A 1 HETATM 16 C C1' SAH . . . J 4 7.814 -18.219 16.711 1 19.51 ? C1' SAH 1846 A 1 HETATM 17 N N9 SAH . . . J 4 9.187 -18.234 17.21 1 19.43 ? N9 SAH 1846 A 1 HETATM 18 C C8 SAH . . . J 4 10.233 -18.55 16.416 1 19.49 ? C8 SAH 1846 A 1 HETATM 19 N N7 SAH . . . J 4 11.341 -18.43 17.147 1 19.02 ? N7 SAH 1846 A 1 HETATM 20 C C5 SAH . . . J 4 11.063 -18.063 18.396 1 19.72 ? C5 SAH 1846 A 1 HETATM 21 C C6 SAH . . . J 4 11.884 -17.831 19.508 1 19.87 ? C6 SAH 1846 A 1 HETATM 22 N N6 SAH . . . J 4 13.208 -17.982 19.445 1 19.56 ? N6 SAH 1846 A 1 HETATM 23 N N1 SAH . . . J 4 11.294 -17.458 20.69 1 19.57 ? N1 SAH 1846 A 1 HETATM 24 C C2 SAH . . . J 4 9.917 -17.321 20.729 1 20.03 ? C2 SAH 1846 A 1 HETATM 25 N N3 SAH . . . J 4 9.119 -17.53 19.609 1 19.14 ? N3 SAH 1846 A 1 HETATM 26 C C4 SAH . . . J 4 9.682 -17.917 18.451 1 19.49 ? C4 SAH 1846 A 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #