data_3OXL # _model_server_result.job_id uLq2v1_Kgvz3O016HW5osw _model_server_result.datetime_utc '2024-12-25 02:44:44' _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 3oxl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":432}' # _entry.id 3OXL # _exptl.entry_id 3OXL _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 3OXL _cell.length_a 55.002 _cell.length_b 101.02 _cell.length_c 117.29 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3OXL _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 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 _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 E _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 52 A CYS 52 1_555 C ZN ZN . A ZN 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc2 A SG CYS 75 A CYS 75 1_555 C ZN ZN . A ZN 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc3 A NE2 HIS 83 A HIS 83 1_555 D ZN ZN . A ZN 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc4 A SG CYS 87 A CYS 87 1_555 D ZN ZN . A ZN 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc5 A SG CYS 208 A CYS 208 1_555 B ZN ZN . A ZN 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.678 ? metalc ? metalc6 A SG CYS 261 A CYS 261 1_555 B ZN ZN . A ZN 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc7 A SG CYS 263 A CYS 263 1_555 B ZN ZN . A ZN 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc8 A SG CYS 266 A CYS 266 1_555 B ZN ZN . A ZN 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? # _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 3OXL _atom_sites.fract_transf_matrix[1][1] 0.018181 _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] 0.009899 _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] 0.008526 _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 1 429 1 ZN ZN . C 2 ZN A 1 430 2 ZN ZN . D 2 ZN A 1 431 3 ZN ZN . E 3 SAH A 1 432 100 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 . . . E 3 -30.437 2.459 -5.632 1 108.49 ? N SAH 432 A 1 HETATM 2 C CA SAH . . . E 3 -28.969 2.175 -5.73 1 108.64 ? CA SAH 432 A 1 HETATM 3 C CB SAH . . . E 3 -28.652 0.823 -5.083 1 108.65 ? CB SAH 432 A 1 HETATM 4 C CG SAH . . . E 3 -27.394 0.8 -4.198 1 108.69 ? CG SAH 432 A 1 HETATM 5 S SD SAH . . . E 3 -26.018 1.722 -4.83 1 109.2 ? SD SAH 432 A 1 HETATM 6 C C SAH . . . E 3 -28.531 2.166 -7.17 1 108.66 ? C SAH 432 A 1 HETATM 7 O O SAH . . . E 3 -27.558 1.493 -7.54 1 108.62 ? O SAH 432 A 1 HETATM 8 O OXT SAH . . . E 3 -29.133 2.835 -8.016 1 108.76 ? OXT SAH 432 A 1 HETATM 9 C C5' SAH . . . E 3 -25.846 2.931 -3.538 1 108.92 ? C5' SAH 432 A 1 HETATM 10 C C4' SAH . . . E 3 -26.509 4.283 -3.85 1 108.07 ? C4' SAH 432 A 1 HETATM 11 O O4' SAH . . . E 3 -27.914 4.295 -3.544 1 107.46 ? O4' SAH 432 A 1 HETATM 12 C C3' SAH . . . E 3 -25.905 5.397 -3.01 1 107.46 ? C3' SAH 432 A 1 HETATM 13 O O3' SAH . . . E 3 -24.881 6.082 -3.744 1 107.67 ? O3' SAH 432 A 1 HETATM 14 C C2' SAH . . . E 3 -27.085 6.274 -2.628 1 106.67 ? C2' SAH 432 A 1 HETATM 15 O O2' SAH . . . E 3 -27.335 7.237 -3.653 1 105.51 ? O2' SAH 432 A 1 HETATM 16 C C1' SAH . . . E 3 -28.261 5.32 -2.606 1 107.17 ? C1' SAH 432 A 1 HETATM 17 N N9 SAH . . . E 3 -28.501 4.696 -1.265 1 107.98 ? N9 SAH 432 A 1 HETATM 18 C C8 SAH . . . E 3 -28.066 3.472 -0.887 1 107.98 ? C8 SAH 432 A 1 HETATM 19 N N7 SAH . . . E 3 -28.446 3.161 0.376 1 108.13 ? N7 SAH 432 A 1 HETATM 20 C C5 SAH . . . E 3 -29.16 4.2 0.846 1 108.13 ? C5 SAH 432 A 1 HETATM 21 C C6 SAH . . . E 3 -29.861 4.518 2.118 1 107.97 ? C6 SAH 432 A 1 HETATM 22 N N6 SAH . . . E 3 -29.867 3.647 3.157 1 107.4 ? N6 SAH 432 A 1 HETATM 23 N N1 SAH . . . E 3 -30.489 5.715 2.205 1 108.49 ? N1 SAH 432 A 1 HETATM 24 C C2 SAH . . . E 3 -30.493 6.596 1.18 1 108.75 ? C2 SAH 432 A 1 HETATM 25 N N3 SAH . . . E 3 -29.876 6.372 -0.002 1 108.72 ? N3 SAH 432 A 1 HETATM 26 C C4 SAH . . . E 3 -29.202 5.21 -0.236 1 108.37 ? C4 SAH 432 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #