data_7VVX # _model_server_result.job_id XEdvZ-3Q7p32A4zz5SbzUw _model_server_result.datetime_utc '2024-11-15 13:49:17' _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 7vvx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 7VVX # _exptl.entry_id 7VVX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _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 7VVX _cell.length_a 66.91 _cell.length_b 131.1 _cell.length_c 134.71 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7VVX _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 ? 2 D N N ? 2 E 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 281 n n N HN1 SAH sing 282 n n N HN2 SAH sing 283 n n CA CB SAH sing 284 n n CA C SAH sing 285 n n CA HA SAH sing 286 n n CB CG SAH sing 287 n n CB HB1 SAH sing 288 n n CB HB2 SAH sing 289 n n CG SD SAH sing 290 n n CG HG1 SAH sing 291 n n CG HG2 SAH sing 292 n n SD C5' SAH sing 293 n n C O SAH doub 294 n n C OXT SAH sing 295 n n OXT HXT SAH sing 296 n n C5' C4' SAH sing 297 n n C5' "H5'1" SAH sing 298 n n C5' "H5'2" SAH sing 299 n n C4' O4' SAH sing 300 n n C4' C3' SAH sing 301 n n C4' H4' SAH sing 302 n n O4' C1' SAH sing 303 n n C3' O3' SAH sing 304 n n C3' C2' SAH sing 305 n n C3' H3' SAH sing 306 n n O3' HO3' SAH sing 307 n n C2' O2' SAH sing 308 n n C2' C1' SAH sing 309 n n C2' H2' SAH sing 310 n n O2' HO2' SAH sing 311 n n C1' N9 SAH sing 312 n n C1' H1' SAH sing 313 n n N9 C8 SAH sing 314 n y N9 C4 SAH sing 315 n y C8 N7 SAH doub 316 n y C8 H8 SAH sing 317 n n N7 C5 SAH sing 318 n y C5 C6 SAH sing 319 n y C5 C4 SAH doub 320 n y C6 N6 SAH sing 321 n n C6 N1 SAH doub 322 n y N6 HN61 SAH sing 323 n n N6 HN62 SAH sing 324 n n N1 C2 SAH sing 325 n y C2 N3 SAH doub 326 n y C2 H2 SAH sing 327 n n N3 C4 SAH sing 328 n y # _atom_sites.entry_id 7VVX _atom_sites.fract_transf_matrix[1][1] 0.014945 _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] 0.007628 _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] 0.007423 _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 D 2 SAH A 1 401 419 SAH SAH . E 2 SAH B 1 401 418 SAH SAH . F 3 MET B 1 402 1 MET MET . G 4 PO4 C 1 401 1 PO4 PO4 . H 5 HOH A 1 501 7 HOH HOH . H 5 HOH A 2 502 3 HOH HOH . H 5 HOH A 3 503 11 HOH HOH . H 5 HOH A 4 504 13 HOH HOH . H 5 HOH A 5 505 6 HOH HOH . H 5 HOH A 6 506 14 HOH HOH . I 5 HOH B 1 501 10 HOH HOH . I 5 HOH B 2 502 4 HOH HOH . I 5 HOH B 3 503 8 HOH HOH . J 5 HOH C 1 501 1 HOH HOH . J 5 HOH C 2 502 2 HOH HOH . J 5 HOH C 3 503 12 HOH HOH . J 5 HOH C 4 504 5 HOH HOH . J 5 HOH C 5 505 15 HOH HOH . J 5 HOH C 6 506 9 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 . . . D 2 36.743 -29.283 -19.287 1 82.29 ? N SAH 401 A 1 HETATM 2 C CA SAH . . . D 2 36.484 -30.566 -19.925 1 87.23 ? CA SAH 401 A 1 HETATM 3 C CB SAH . . . D 2 37.384 -30.795 -21.151 1 92.22 ? CB SAH 401 A 1 HETATM 4 C CG SAH . . . D 2 36.966 -30.056 -22.432 1 86.49 ? CG SAH 401 A 1 HETATM 5 S SD SAH . . . D 2 38.081 -30.207 -23.87 1 91.59 ? SD SAH 401 A 1 HETATM 6 C C SAH . . . D 2 36.649 -31.711 -18.924 1 91.13 ? C SAH 401 A 1 HETATM 7 O O SAH . . . D 2 36.369 -32.877 -19.246 1 88.57 ? O SAH 401 A 1 HETATM 8 O OXT SAH . . . D 2 37.052 -31.502 -17.775 1 89.16 ? OXT SAH 401 A 1 HETATM 9 C C5' SAH . . . D 2 37.504 -31.871 -24.303 1 89.03 ? C5' SAH 401 A 1 HETATM 10 C C4' SAH . . . D 2 37.668 -32.102 -25.8 1 89.73 ? C4' SAH 401 A 1 HETATM 11 O O4' SAH . . . D 2 37.039 -31.039 -26.507 1 89.31 ? O4' SAH 401 A 1 HETATM 12 C C3' SAH . . . D 2 39.136 -32.103 -26.239 1 90.22 ? C3' SAH 401 A 1 HETATM 13 O O3' SAH . . . D 2 39.47 -33.306 -26.901 1 86.84 ? O3' SAH 401 A 1 HETATM 14 C C2' SAH . . . D 2 39.271 -30.977 -27.246 1 89.08 ? C2' SAH 401 A 1 HETATM 15 O O2' SAH . . . D 2 40.016 -31.394 -28.368 1 88.02 ? O2' SAH 401 A 1 HETATM 16 C C1' SAH . . . D 2 37.83 -30.678 -27.635 1 87.14 ? C1' SAH 401 A 1 HETATM 17 N N9 SAH . . . D 2 37.613 -29.266 -28.025 1 87.97 ? N9 SAH 401 A 1 HETATM 18 C C8 SAH . . . D 2 38.194 -28.148 -27.468 1 83.36 ? C8 SAH 401 A 1 HETATM 19 N N7 SAH . . . D 2 37.727 -27.054 -28.122 1 80.23 ? N7 SAH 401 A 1 HETATM 20 C C5 SAH . . . D 2 36.857 -27.451 -29.078 1 78.31 ? C5 SAH 401 A 1 HETATM 21 C C6 SAH . . . D 2 36.109 -26.741 -30.004 1 74.65 ? C6 SAH 401 A 1 HETATM 22 N N6 SAH . . . D 2 36.177 -25.412 -30.05 1 80.17 ? N6 SAH 401 A 1 HETATM 23 N N1 SAH . . . D 2 35.293 -27.428 -30.875 1 69.46 ? N1 SAH 401 A 1 HETATM 24 C C2 SAH . . . D 2 35.221 -28.811 -30.832 1 73.56 ? C2 SAH 401 A 1 HETATM 25 N N3 SAH . . . D 2 35.969 -29.531 -29.918 1 76.13 ? N3 SAH 401 A 1 HETATM 26 C C4 SAH . . . D 2 36.774 -28.846 -29.043 1 86.93 ? C4 SAH 401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 26 #