data_3AV5 # _model_server_result.job_id MDTBAGkXfMO1WmGdSRtDKQ _model_server_result.datetime_utc '2025-03-04 08:50:12' _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 3av5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1}' # _entry.id 3AV5 # _exptl.entry_id 3AV5 _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 90 _cell.entry_id 3AV5 _cell.length_a 134.993 _cell.length_b 96.92 _cell.length_c 130.615 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3AV5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A SG CYS 69 A CYS 359 1_555 B ZN ZN . A ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc2 A SG CYS 72 A CYS 362 1_555 B ZN ZN . A ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc3 A SG CYS 130 A CYS 420 1_555 B ZN ZN . A ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? metalc ? metalc4 A ND1 HIS 134 A HIS 424 1_555 B ZN ZN . A ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc5 A SG CYS 366 A CYS 656 1_555 C ZN ZN . A ZN 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc6 A SG CYS 369 A CYS 659 1_555 C ZN ZN . A ZN 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc7 A SG CYS 372 A CYS 662 1_555 C ZN ZN . A ZN 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc8 A SG CYS 404 A CYS 694 1_555 C ZN ZN . A ZN 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc9 A NE2 HIS 506 A HIS 796 1_555 D ZN ZN . A ZN 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc10 A SG CYS 533 A CYS 823 1_555 D ZN ZN . A ZN 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc11 A SG CYS 607 A CYS 897 1_555 D ZN ZN . A ZN 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc12 A SG CYS 610 A CYS 900 1_555 D ZN ZN . A ZN 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc13 A SG CYS 1189 A CYS 1479 1_555 E ZN ZN . A ZN 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc14 A SG CYS 1191 A CYS 1481 1_555 E ZN ZN . A ZN 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc15 A SG CYS 1197 A CYS 1487 1_555 E ZN ZN . A ZN 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc16 A NE2 HIS 1214 A HIS 1504 1_555 E ZN ZN . A ZN 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? # _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 3AV5 _atom_sites.fract_transf_matrix[1][1] 0.007408 _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] 0.010318 _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] 0.007656 _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 ZN A 1 2001 2001 ZN ZN . C 2 ZN A 1 2002 2002 ZN ZN . D 2 ZN A 1 2004 2004 ZN ZN . E 2 ZN A 1 2005 2005 ZN ZN . F 3 SAH A 1 1 1 SAH SAH . # 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 . . . F 3 81.922 14.038 35.893 1 48.71 ? N SAH 1 A 1 HETATM 2 C CA SAH . . . F 3 81.534 13.942 34.464 1 49.08 ? CA SAH 1 A 1 HETATM 3 C CB SAH . . . F 3 80.435 14.877 33.962 1 45.63 ? CB SAH 1 A 1 HETATM 4 C CG SAH . . . F 3 79.136 14.447 34.662 1 43.6 ? CG SAH 1 A 1 HETATM 5 S SD SAH . . . F 3 77.662 14.587 33.598 1 39.94 ? SD SAH 1 A 1 HETATM 6 C C SAH . . . F 3 82.68 13.791 33.498 1 51.54 ? C SAH 1 A 1 HETATM 7 O O SAH . . . F 3 82.497 12.987 32.583 1 52.9 ? O SAH 1 A 1 HETATM 8 O OXT SAH . . . F 3 83.823 14.487 33.602 1 51.55 ? OXT SAH 1 A 1 HETATM 9 C C5' SAH . . . F 3 76.3 14.383 34.754 1 38.43 ? C5' SAH 1 A 1 HETATM 10 C C4' SAH . . . F 3 75.941 12.912 34.862 1 40.21 ? C4' SAH 1 A 1 HETATM 11 O O4' SAH . . . F 3 74.814 12.818 35.695 1 38.88 ? O4' SAH 1 A 1 HETATM 12 C C3' SAH . . . F 3 75.439 12.318 33.555 1 40.84 ? C3' SAH 1 A 1 HETATM 13 O O3' SAH . . . F 3 76.487 11.549 32.915 1 42.72 ? O3' SAH 1 A 1 HETATM 14 C C2' SAH . . . F 3 74.123 11.551 34.002 1 40.44 ? C2' SAH 1 A 1 HETATM 15 O O2' SAH . . . F 3 73.827 10.294 33.339 1 43.05 ? O2' SAH 1 A 1 HETATM 16 C C1' SAH . . . F 3 74.374 11.472 35.525 1 41.02 ? C1' SAH 1 A 1 HETATM 17 N N9 SAH . . . F 3 73.251 11.413 36.422 1 40.55 ? N9 SAH 1 A 1 HETATM 18 C C8 SAH . . . F 3 72.147 12.176 36.285 1 38.83 ? C8 SAH 1 A 1 HETATM 19 N N7 SAH . . . F 3 71.339 11.955 37.254 1 39.51 ? N7 SAH 1 A 1 HETATM 20 C C5 SAH . . . F 3 71.897 11.082 38.141 1 40.19 ? C5 SAH 1 A 1 HETATM 21 C C6 SAH . . . F 3 71.459 10.53 39.388 1 40.8 ? C6 SAH 1 A 1 HETATM 22 N N6 SAH . . . F 3 70.196 10.879 39.903 1 39.88 ? N6 SAH 1 A 1 HETATM 23 N N1 SAH . . . F 3 72.279 9.625 39.99 1 42.2 ? N1 SAH 1 A 1 HETATM 24 C C2 SAH . . . F 3 73.49 9.285 39.455 1 43.94 ? C2 SAH 1 A 1 HETATM 25 N N3 SAH . . . F 3 73.919 9.816 38.285 1 42.89 ? N3 SAH 1 A 1 HETATM 26 C C4 SAH . . . F 3 73.161 10.716 37.607 1 41.55 ? C4 SAH 1 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #