data_8RYD # _model_server_result.job_id b_0-KyQ-UhPFOLGFTCrZ0A _model_server_result.datetime_utc '2025-01-08 18:02:48' _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 8ryd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":901}' # _entry.id 8RYD # _exptl.entry_id 8RYD _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 4 _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 8RYD _cell.length_a 141.5 _cell.length_b 84.15 _cell.length_c 94.34 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RYD _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_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,E,F,I,J 1 1 C,G,K 2 1 D,H,L 2 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H 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 . _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _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 N CA SAH sing 277 n n N HN1 SAH sing 278 n n N HN2 SAH sing 279 n n CA CB SAH sing 280 n n CA C SAH sing 281 n n CA HA SAH sing 282 n n CB CG SAH sing 283 n n CB HB1 SAH sing 284 n n CB HB2 SAH sing 285 n n CG SD SAH sing 286 n n CG HG1 SAH sing 287 n n CG HG2 SAH sing 288 n n SD C5' SAH sing 289 n n C O SAH doub 290 n n C OXT SAH sing 291 n n OXT HXT SAH sing 292 n n C5' C4' SAH sing 293 n n C5' "H5'1" SAH sing 294 n n C5' "H5'2" SAH sing 295 n n C4' O4' SAH sing 296 n n C4' C3' SAH sing 297 n n C4' H4' SAH sing 298 n n O4' C1' SAH sing 299 n n C3' O3' SAH sing 300 n n C3' C2' SAH sing 301 n n C3' H3' SAH sing 302 n n O3' HO3' SAH sing 303 n n C2' O2' SAH sing 304 n n C2' C1' SAH sing 305 n n C2' H2' SAH sing 306 n n O2' HO2' SAH sing 307 n n C1' N9 SAH sing 308 n n C1' H1' SAH sing 309 n n N9 C8 SAH sing 310 n y N9 C4 SAH sing 311 n y C8 N7 SAH doub 312 n y C8 H8 SAH sing 313 n n N7 C5 SAH sing 314 n y C5 C6 SAH sing 315 n y C5 C4 SAH doub 316 n y C6 N6 SAH sing 317 n n C6 N1 SAH doub 318 n y N6 HN61 SAH sing 319 n n N6 HN62 SAH sing 320 n n N1 C2 SAH sing 321 n y C2 N3 SAH doub 322 n y C2 H2 SAH sing 323 n n N3 C4 SAH sing 324 n y # _atom_sites.entry_id 8RYD _atom_sites.fract_transf_matrix[1][1] 0.007067 _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] 0.011884 _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] 0.0106 _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 SAH A 1 901 901 SAH SAH . F 2 SAH B 1 901 901 SAH SAH . G 2 SAH C 1 901 901 SAH SAH . H 2 SAH D 1 901 901 SAH SAH . I 3 HOH A 1 1001 4 HOH HOH . J 3 HOH B 1 1001 12 HOH HOH . J 3 HOH B 2 1002 7 HOH HOH . J 3 HOH B 3 1003 11 HOH HOH . K 3 HOH C 1 1001 1 HOH HOH . K 3 HOH C 2 1002 5 HOH HOH . K 3 HOH C 3 1003 14 HOH HOH . K 3 HOH C 4 1004 16 HOH HOH . K 3 HOH C 5 1005 9 HOH HOH . K 3 HOH C 6 1006 15 HOH HOH . K 3 HOH C 7 1007 13 HOH HOH . L 3 HOH D 1 1001 10 HOH HOH . L 3 HOH D 2 1002 6 HOH HOH . L 3 HOH D 3 1003 3 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 . . . E 2 -18.514 22.262 -24.38 1 77.33 ? N SAH 901 A 1 HETATM 2 C CA SAH . . . E 2 -19.879 22.486 -24.951 1 78.35 ? CA SAH 901 A 1 HETATM 3 C CB SAH . . . E 2 -20.117 21.601 -26.18 1 76.89 ? CB SAH 901 A 1 HETATM 4 C CG SAH . . . E 2 -19.012 21.69 -27.214 1 75.96 ? CG SAH 901 A 1 HETATM 5 S SD SAH . . . E 2 -19.476 21.039 -28.839 1 75.08 ? SD SAH 901 A 1 HETATM 6 C C SAH . . . E 2 -20.938 22.173 -23.886 1 80.63 ? C SAH 901 A 1 HETATM 7 O O SAH . . . E 2 -20.64 22.061 -22.697 1 81.24 ? O SAH 901 A 1 HETATM 8 O OXT SAH . . . E 2 -22.12 22.026 -24.195 1 82.19 ? OXT SAH 901 A 1 HETATM 9 C C5' SAH . . . E 2 -17.853 20.925 -29.63 1 73.14 ? C5' SAH 901 A 1 HETATM 10 C C4' SAH . . . E 2 -17.848 20.92 -31.141 1 72.07 ? C4' SAH 901 A 1 HETATM 11 O O4' SAH . . . E 2 -18.947 20.116 -31.624 1 71.57 ? O4' SAH 901 A 1 HETATM 12 C C3' SAH . . . E 2 -18.006 22.296 -31.8 1 72.24 ? C3' SAH 901 A 1 HETATM 13 O O3' SAH . . . E 2 -16.867 22.602 -32.595 1 71.21 ? O3' SAH 901 A 1 HETATM 14 C C2' SAH . . . E 2 -19.259 22.16 -32.675 1 72.42 ? C2' SAH 901 A 1 HETATM 15 O O2' SAH . . . E 2 -19.139 22.813 -33.921 1 72.11 ? O2' SAH 901 A 1 HETATM 16 C C1' SAH . . . E 2 -19.344 20.651 -32.86 1 71.81 ? C1' SAH 901 A 1 HETATM 17 N N9 SAH . . . E 2 -20.679 20.165 -33.183 1 72.34 ? N9 SAH 901 A 1 HETATM 18 C C8 SAH . . . E 2 -21.781 20.167 -32.366 1 73.19 ? C8 SAH 901 A 1 HETATM 19 N N7 SAH . . . E 2 -22.848 19.663 -32.933 1 73.97 ? N7 SAH 901 A 1 HETATM 20 C C5 SAH . . . E 2 -22.424 19.305 -34.205 1 72.96 ? C5 SAH 901 A 1 HETATM 21 C C6 SAH . . . E 2 -23.091 18.715 -35.296 1 73.34 ? C6 SAH 901 A 1 HETATM 22 N N6 SAH . . . E 2 -24.375 18.369 -35.275 1 73.73 ? N6 SAH 901 A 1 HETATM 23 N N1 SAH . . . E 2 -22.372 18.492 -36.422 1 73.45 ? N1 SAH 901 A 1 HETATM 24 C C2 SAH . . . E 2 -21.079 18.843 -36.436 1 71.96 ? C2 SAH 901 A 1 HETATM 25 N N3 SAH . . . E 2 -20.35 19.402 -35.475 1 70.54 ? N3 SAH 901 A 1 HETATM 26 C C4 SAH . . . E 2 -21.087 19.611 -34.371 1 72.2 ? C4 SAH 901 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 26 #