data_3OXF # _model_server_result.job_id oNVdmiE7DDq3iY0nRz9zcg _model_server_result.datetime_utc '2024-11-04 20:32:10' _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 3oxf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":437}' # _entry.id 3OXF # _exptl.entry_id 3OXF _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 91.78 _cell.angle_gamma 90 _cell.entry_id 3OXF _cell.length_a 57.991 _cell.length_b 117.99 _cell.length_c 82.808 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3OXF _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,C,D,E,F,K 1 1 B,G,H,I,J,L 2 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 G 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 metalc ? metalc1 A SG CYS 49 A CYS 49 1_555 D ZN ZN . A ZN 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc2 A SG CYS 52 A CYS 52 1_555 D ZN ZN . A ZN 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc3 A SG CYS 62 A CYS 62 1_555 E ZN ZN . A ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc4 A SG CYS 65 A CYS 65 1_555 E ZN ZN . A ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc5 A SG CYS 71 A CYS 71 1_555 D ZN ZN . A ZN 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc6 A SG CYS 75 A CYS 75 1_555 D ZN ZN . A ZN 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc7 A NE2 HIS 83 A HIS 83 1_555 E ZN ZN . A ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc8 A SG CYS 87 A CYS 87 1_555 E ZN ZN . A ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc9 A SG CYS 208 A CYS 208 1_555 F ZN ZN . A ZN 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc10 A SG CYS 261 A CYS 261 1_555 F ZN ZN . A ZN 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc11 A SG CYS 263 A CYS 263 1_555 F ZN ZN . A ZN 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc12 A SG CYS 266 A CYS 266 1_555 F ZN ZN . A ZN 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc13 B SG CYS 49 B CYS 49 1_555 H ZN ZN . B ZN 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc14 B SG CYS 52 B CYS 52 1_555 H ZN ZN . B ZN 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc15 B SG CYS 62 B CYS 62 1_555 I ZN ZN . B ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc16 B SG CYS 65 B CYS 65 1_555 I ZN ZN . B ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc17 B SG CYS 71 B CYS 71 1_555 H ZN ZN . B ZN 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc18 B SG CYS 75 B CYS 75 1_555 H ZN ZN . B ZN 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc19 B NE2 HIS 83 B HIS 83 1_555 I ZN ZN . B ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc20 B SG CYS 87 B CYS 87 1_555 I ZN ZN . B ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc21 B SG CYS 208 B CYS 208 1_555 J ZN ZN . B ZN 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc22 B SG CYS 261 B CYS 261 1_555 J ZN ZN . B ZN 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc23 B SG CYS 263 B CYS 263 1_555 J ZN ZN . B ZN 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc24 B SG CYS 266 B CYS 266 1_555 J ZN ZN . B ZN 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? # _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 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 3OXF _atom_sites.fract_transf_matrix[1][1] 0.017244 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000536 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008475 _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] 0.012082 _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 1 437 100 SAH SAH . D 3 ZN A 1 438 101 ZN ZN . E 3 ZN A 1 439 102 ZN ZN . F 3 ZN A 1 440 103 ZN ZN . G 2 SAH B 1 437 200 SAH SAH . H 3 ZN B 1 438 201 ZN ZN . I 3 ZN B 1 439 202 ZN ZN . J 3 ZN B 1 440 203 ZN ZN . K 4 HOH A 1 441 1 HOH HOH . K 4 HOH A 2 442 2 HOH HOH . K 4 HOH A 3 443 3 HOH HOH . K 4 HOH A 4 444 4 HOH HOH . K 4 HOH A 5 445 5 HOH HOH . K 4 HOH A 6 446 6 HOH HOH . K 4 HOH A 7 447 7 HOH HOH . K 4 HOH A 8 448 8 HOH HOH . K 4 HOH A 9 449 13 HOH HOH . K 4 HOH A 10 450 14 HOH HOH . K 4 HOH A 11 451 15 HOH HOH . K 4 HOH A 12 452 16 HOH HOH . K 4 HOH A 13 453 17 HOH HOH . K 4 HOH A 14 454 20 HOH HOH . K 4 HOH A 15 455 23 HOH HOH . K 4 HOH A 16 456 24 HOH HOH . L 4 HOH B 1 441 9 HOH HOH . L 4 HOH B 2 442 10 HOH HOH . L 4 HOH B 3 443 11 HOH HOH . L 4 HOH B 4 444 12 HOH HOH . L 4 HOH B 5 445 18 HOH HOH . L 4 HOH B 6 446 19 HOH HOH . L 4 HOH B 7 447 21 HOH HOH . L 4 HOH B 8 448 22 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 . . . G 2 56.304 -36.087 57.698 1 44.83 ? N SAH 437 B 1 HETATM 2 C CA SAH . . . G 2 56.054 -35.265 56.481 1 45.1 ? CA SAH 437 B 1 HETATM 3 C CB SAH . . . G 2 54.75 -35.692 55.808 1 45.05 ? CB SAH 437 B 1 HETATM 4 C CG SAH . . . G 2 54.955 -36.801 54.773 1 45.59 ? CG SAH 437 B 1 HETATM 5 S SD SAH . . . G 2 56.009 -36.315 53.43 1 45.72 ? SD SAH 437 B 1 HETATM 6 C C SAH . . . G 2 56.011 -33.817 56.862 1 45.2 ? C SAH 437 B 1 HETATM 7 O O SAH . . . G 2 56.468 -33.452 57.946 1 45.42 ? O SAH 437 B 1 HETATM 8 O OXT SAH . . . G 2 55.534 -32.959 56.111 1 45.3 ? OXT SAH 437 B 1 HETATM 9 C C5' SAH . . . G 2 57.209 -37.616 53.424 1 46.38 ? C5' SAH 437 B 1 HETATM 10 C C4' SAH . . . G 2 58.235 -37.473 54.545 1 46.52 ? C4' SAH 437 B 1 HETATM 11 O O4' SAH . . . G 2 57.647 -37.81 55.806 1 46.4 ? O4' SAH 437 B 1 HETATM 12 C C3' SAH . . . G 2 59.417 -38.418 54.38 1 46.72 ? C3' SAH 437 B 1 HETATM 13 O O3' SAH . . . G 2 60.495 -37.793 53.676 1 46.98 ? O3' SAH 437 B 1 HETATM 14 C C2' SAH . . . G 2 59.811 -38.762 55.801 1 46.62 ? C2' SAH 437 B 1 HETATM 15 O O2' SAH . . . G 2 60.764 -37.823 56.308 1 46.46 ? O2' SAH 437 B 1 HETATM 16 C C1' SAH . . . G 2 58.53 -38.605 56.598 1 46.54 ? C1' SAH 437 B 1 HETATM 17 N N9 SAH . . . G 2 57.927 -39.938 56.859 1 46.53 ? N9 SAH 437 B 1 HETATM 18 C C8 SAH . . . G 2 56.823 -40.442 56.271 1 46.92 ? C8 SAH 437 B 1 HETATM 19 N N7 SAH . . . G 2 56.536 -41.689 56.729 1 46.51 ? N7 SAH 437 B 1 HETATM 20 C C5 SAH . . . G 2 57.48 -42.004 57.638 1 46.06 ? C5 SAH 437 B 1 HETATM 21 C C6 SAH . . . G 2 57.782 -43.163 58.512 1 45.34 ? C6 SAH 437 B 1 HETATM 22 N N6 SAH . . . G 2 57.003 -44.268 58.504 1 45.02 ? N6 SAH 437 B 1 HETATM 23 N N1 SAH . . . G 2 58.864 -43.083 59.315 1 45.47 ? N1 SAH 437 B 1 HETATM 24 C C2 SAH . . . G 2 59.659 -41.996 59.341 1 45.76 ? C2 SAH 437 B 1 HETATM 25 N N3 SAH . . . G 2 59.447 -40.91 58.575 1 46.2 ? N3 SAH 437 B 1 HETATM 26 C C4 SAH . . . G 2 58.393 -40.85 57.72 1 46.35 ? C4 SAH 437 B 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 26 #