data_8RYD # _model_server_result.job_id 0MYQ1nE76wpZ5J_9c3d89g _model_server_result.datetime_utc '2025-01-08 17:38:09' _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":"H","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 . . . H 2 -28.499 2.92 26.554 1 72.89 ? N SAH 901 D 1 HETATM 2 C CA SAH . . . H 2 -29.61 3.708 27.155 1 74.41 ? CA SAH 901 D 1 HETATM 3 C CB SAH . . . H 2 -29.152 4.446 28.419 1 74.31 ? CB SAH 901 D 1 HETATM 4 C CG SAH . . . H 2 -28.522 3.542 29.465 1 73.13 ? CG SAH 901 D 1 HETATM 5 S SD SAH . . . H 2 -28.526 4.255 31.131 1 72.49 ? SD SAH 901 D 1 HETATM 6 C C SAH . . . H 2 -30.125 4.726 26.13 1 76.76 ? C SAH 901 D 1 HETATM 7 O O SAH . . . H 2 -29.809 4.652 24.941 1 78.61 ? O SAH 901 D 1 HETATM 8 O OXT SAH . . . H 2 -30.87 5.646 26.47 1 78.63 ? OXT SAH 901 D 1 HETATM 9 C C5' SAH . . . H 2 -27.153 3.374 31.914 1 70.16 ? C5' SAH 901 D 1 HETATM 10 C C4' SAH . . . H 2 -27.239 3.262 33.419 1 70.27 ? C4' SAH 901 D 1 HETATM 11 O O4' SAH . . . H 2 -27.263 4.587 33.991 1 71.07 ? O4' SAH 901 D 1 HETATM 12 C C3' SAH . . . H 2 -28.483 2.543 33.959 1 70.84 ? C3' SAH 901 D 1 HETATM 13 O O3' SAH . . . H 2 -28.108 1.406 34.726 1 70.41 ? O3' SAH 901 D 1 HETATM 14 C C2' SAH . . . H 2 -29.176 3.589 34.843 1 71.91 ? C2' SAH 901 D 1 HETATM 15 O O2' SAH . . . H 2 -29.719 3.045 36.026 1 71.03 ? O2' SAH 901 D 1 HETATM 16 C C1' SAH . . . H 2 -28.026 4.532 35.17 1 72 ? C1' SAH 901 D 1 HETATM 17 N N9 SAH . . . H 2 -28.44 5.883 35.527 1 74.19 ? N9 SAH 901 D 1 HETATM 18 C C8 SAH . . . H 2 -29.162 6.757 34.754 1 75.01 ? C8 SAH 901 D 1 HETATM 19 N N7 SAH . . . H 2 -29.384 7.907 35.338 1 76.36 ? N7 SAH 901 D 1 HETATM 20 C C5 SAH . . . H 2 -28.768 7.788 36.576 1 75.9 ? C5 SAH 901 D 1 HETATM 21 C C6 SAH . . . H 2 -28.647 8.675 37.663 1 78.09 ? C6 SAH 901 D 1 HETATM 22 N N6 SAH . . . H 2 -29.159 9.902 37.672 1 80.97 ? N6 SAH 901 D 1 HETATM 23 N N1 SAH . . . H 2 -27.965 8.242 38.751 1 77.17 ? N1 SAH 901 D 1 HETATM 24 C C2 SAH . . . H 2 -27.452 7.005 38.733 1 75.05 ? C2 SAH 901 D 1 HETATM 25 N N3 SAH . . . H 2 -27.502 6.088 37.771 1 74.25 ? N3 SAH 901 D 1 HETATM 26 C C4 SAH . . . H 2 -28.182 6.543 36.705 1 75.05 ? C4 SAH 901 D 1 # _model_server_stats.io_time_ms 81 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 228 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 26 #