data_5N0Q # _model_server_result.job_id U55y0cMJ9j1uCneoxTTWTQ _model_server_result.datetime_utc '2025-03-04 12:04:31' _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 5n0q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 5N0Q # _exptl.entry_id 5N0Q _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 5N0Q _cell.length_a 72.443 _cell.length_b 102.424 _cell.length_c 115.297 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5N0Q _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N 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 covale ? covale1 A C MVA 402 A MVA 403 1_555 A N MVA 403 A MVA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale2 A C MVA 403 A MVA 404 1_555 A N SAR 404 A SAR 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale3 A C SAR 404 A SAR 405 1_555 A N MVA 405 A MVA 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale4 A C MVA 405 A MVA 406 1_555 A N IML 406 A IML 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale5 A C IML 406 A IML 407 1_555 A N SAR 407 A SAR 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale6 A C SAR 407 A SAR 408 1_555 A N VAL 408 A VAL 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale7 B C MVA 405 B MVA 406 1_555 B N IML 406 B IML 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale8 B C IML 406 B IML 407 1_555 B N SAR 407 B SAR 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale9 B C SAR 407 B SAR 408 1_555 B N VAL 408 B VAL 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? # _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 322 n n N HN1 SAH sing 323 n n N HN2 SAH sing 324 n n CA CB SAH sing 325 n n CA C SAH sing 326 n n CA HA SAH sing 327 n n CB CG SAH sing 328 n n CB HB1 SAH sing 329 n n CB HB2 SAH sing 330 n n CG SD SAH sing 331 n n CG HG1 SAH sing 332 n n CG HG2 SAH sing 333 n n SD C5' SAH sing 334 n n C O SAH doub 335 n n C OXT SAH sing 336 n n OXT HXT SAH sing 337 n n C5' C4' SAH sing 338 n n C5' "H5'1" SAH sing 339 n n C5' "H5'2" SAH sing 340 n n C4' O4' SAH sing 341 n n C4' C3' SAH sing 342 n n C4' H4' SAH sing 343 n n O4' C1' SAH sing 344 n n C3' O3' SAH sing 345 n n C3' C2' SAH sing 346 n n C3' H3' SAH sing 347 n n O3' HO3' SAH sing 348 n n C2' O2' SAH sing 349 n n C2' C1' SAH sing 350 n n C2' H2' SAH sing 351 n n O2' HO2' SAH sing 352 n n C1' N9 SAH sing 353 n n C1' H1' SAH sing 354 n n N9 C8 SAH sing 355 n y N9 C4 SAH sing 356 n y C8 N7 SAH doub 357 n y C8 H8 SAH sing 358 n n N7 C5 SAH sing 359 n y C5 C6 SAH sing 360 n y C5 C4 SAH doub 361 n y C6 N6 SAH sing 362 n n C6 N1 SAH doub 363 n y N6 HN61 SAH sing 364 n n N6 HN62 SAH sing 365 n n N1 C2 SAH sing 366 n y C2 N3 SAH doub 367 n y C2 H2 SAH sing 368 n n N3 C4 SAH sing 369 n y # _atom_sites.entry_id 5N0Q _atom_sites.fract_transf_matrix[1][1] 0.013804 _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] 0.009763 _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] 0.008673 _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 C 2 SAH A 1 501 501 SAH SAH . D 2 SAH B 1 501 501 SAH SAH . E 3 HOH A 1 601 11 HOH HOH . E 3 HOH A 2 602 7 HOH HOH . E 3 HOH A 3 603 2 HOH HOH . E 3 HOH A 4 604 15 HOH HOH . E 3 HOH A 5 605 14 HOH HOH . E 3 HOH A 6 606 3 HOH HOH . E 3 HOH A 7 607 6 HOH HOH . F 3 HOH B 1 601 10 HOH HOH . F 3 HOH B 2 602 12 HOH HOH . F 3 HOH B 3 603 1 HOH HOH . F 3 HOH B 4 604 4 HOH HOH . F 3 HOH B 5 605 9 HOH HOH . F 3 HOH B 6 606 8 HOH HOH . F 3 HOH B 7 607 5 HOH HOH . F 3 HOH B 8 608 13 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 -23.113 11.654 -24.802 1 46.6 ? N SAH 501 B 1 HETATM 2 C CA SAH . . . D 2 -22.54 11.905 -26.117 1 48.6 ? CA SAH 501 B 1 HETATM 3 C CB SAH . . . D 2 -22.812 13.343 -26.56 1 54.17 ? CB SAH 501 B 1 HETATM 4 C CG SAH . . . D 2 -24.29 13.652 -26.799 1 59.34 ? CG SAH 501 B 1 HETATM 5 S SD SAH . . . D 2 -24.634 15.393 -27.179 1 54.72 ? SD SAH 501 B 1 HETATM 6 C C SAH . . . D 2 -21.046 11.605 -26.097 1 58.82 ? C SAH 501 B 1 HETATM 7 O O SAH . . . D 2 -20.317 11.89 -27.047 1 62.51 ? O SAH 501 B 1 HETATM 8 O OXT SAH . . . D 2 -20.535 11.063 -25.117 1 64.35 ? OXT SAH 501 B 1 HETATM 9 C C5' SAH . . . D 2 -24.471 15.102 -28.961 1 56.56 ? C5' SAH 501 B 1 HETATM 10 C C4' SAH . . . D 2 -23.167 15.657 -29.526 1 61.53 ? C4' SAH 501 B 1 HETATM 11 O O4' SAH . . . D 2 -22.127 14.693 -29.455 1 65.47 ? O4' SAH 501 B 1 HETATM 12 C C3' SAH . . . D 2 -23.284 16.04 -30.993 1 58.39 ? C3' SAH 501 B 1 HETATM 13 O O3' SAH . . . D 2 -23.714 17.37 -31.162 1 51.74 ? O3' SAH 501 B 1 HETATM 14 C C2' SAH . . . D 2 -21.882 15.837 -31.522 1 56.31 ? C2' SAH 501 B 1 HETATM 15 O O2' SAH . . . D 2 -21.122 17.013 -31.391 1 54.6 ? O2' SAH 501 B 1 HETATM 16 C C1' SAH . . . D 2 -21.298 14.786 -30.601 1 63.11 ? C1' SAH 501 B 1 HETATM 17 N N9 SAH . . . D 2 -21.298 13.52 -31.351 1 58.81 ? N9 SAH 501 B 1 HETATM 18 C C8 SAH . . . D 2 -22.243 12.528 -31.278 1 61.67 ? C8 SAH 501 B 1 HETATM 19 N N7 SAH . . . D 2 -21.898 11.54 -32.136 1 59.23 ? N7 SAH 501 B 1 HETATM 20 C C5 SAH . . . D 2 -20.755 11.894 -32.765 1 63.63 ? C5 SAH 501 B 1 HETATM 21 C C6 SAH . . . D 2 -19.98 11.261 -33.727 1 63.36 ? C6 SAH 501 B 1 HETATM 22 N N6 SAH . . . D 2 -20.336 10.069 -34.197 1 63.2 ? N6 SAH 501 B 1 HETATM 23 N N1 SAH . . . D 2 -18.839 11.879 -34.193 1 65.76 ? N1 SAH 501 B 1 HETATM 24 C C2 SAH . . . D 2 -18.471 13.114 -33.705 1 60.92 ? C2 SAH 501 B 1 HETATM 25 N N3 SAH . . . D 2 -19.248 13.736 -32.75 1 59.81 ? N3 SAH 501 B 1 HETATM 26 C C4 SAH . . . D 2 -20.368 13.138 -32.284 1 57.93 ? C4 SAH 501 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 26 #