data_8XDV # _model_server_result.job_id d5VyE7aLZkyI_MipH4Sfug _model_server_result.datetime_utc '2024-10-12 16:32:47' _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 8xdv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 8XDV # _exptl.entry_id 8XDV _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 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 8XDV _cell.length_a 49.951 _cell.length_b 80.894 _cell.length_c 116.107 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8XDV _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall 'P 2 2ab (z,x,y)' _symmetry.space_group_name_H-M 'P 2 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,G,H _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 ? 3 D N N ? 3 F 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 OD1 ASP 158 A ASP 155 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc2 A OD2 ASP 184 A ASP 181 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc3 A OD1 ASN 185 A ASN 182 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc4 C MG MG . A MG 301 1_555 G O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc5 C MG MG . A MG 301 1_555 G O HOH . A HOH 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc6 C MG MG . A MG 301 1_555 G O HOH . A HOH 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc7 B OD1 ASP 158 B ASP 155 1_555 E MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc8 B OD2 ASP 184 B ASP 181 1_555 E MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc9 B OD1 ASN 185 B ASN 182 1_555 E MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc10 E MG MG . B MG 301 1_555 H O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc11 E MG MG . B MG 301 1_555 H O HOH . B HOH 415 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc12 E MG MG . B MG 301 1_555 H O HOH . B HOH 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? # _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 8XDV _atom_sites.fract_transf_matrix[1][1] 0.02002 _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] 0.012362 _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] 0.008613 _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 MG A 1 301 301 MG MG . D 3 SAH A 1 302 401 SAH SAH . E 2 MG B 1 301 301 MG MG . F 3 SAH B 1 302 401 SAH SAH . G 4 HOH A 1 401 32 HOH HOH . G 4 HOH A 2 402 6 HOH HOH . G 4 HOH A 3 403 13 HOH HOH . G 4 HOH A 4 404 80 HOH HOH . G 4 HOH A 5 405 7 HOH HOH . G 4 HOH A 6 406 41 HOH HOH . G 4 HOH A 7 407 20 HOH HOH . G 4 HOH A 8 408 15 HOH HOH . G 4 HOH A 9 409 34 HOH HOH . G 4 HOH A 10 410 19 HOH HOH . G 4 HOH A 11 411 5 HOH HOH . G 4 HOH A 12 412 38 HOH HOH . G 4 HOH A 13 413 66 HOH HOH . G 4 HOH A 14 414 56 HOH HOH . G 4 HOH A 15 415 75 HOH HOH . G 4 HOH A 16 416 55 HOH HOH . G 4 HOH A 17 417 10 HOH HOH . G 4 HOH A 18 418 73 HOH HOH . G 4 HOH A 19 419 52 HOH HOH . G 4 HOH A 20 420 3 HOH HOH . G 4 HOH A 21 421 9 HOH HOH . G 4 HOH A 22 422 57 HOH HOH . G 4 HOH A 23 423 31 HOH HOH . G 4 HOH A 24 424 2 HOH HOH . G 4 HOH A 25 425 51 HOH HOH . G 4 HOH A 26 426 21 HOH HOH . G 4 HOH A 27 427 86 HOH HOH . G 4 HOH A 28 428 61 HOH HOH . G 4 HOH A 29 429 25 HOH HOH . G 4 HOH A 30 430 24 HOH HOH . G 4 HOH A 31 431 11 HOH HOH . G 4 HOH A 32 432 16 HOH HOH . G 4 HOH A 33 433 40 HOH HOH . G 4 HOH A 34 434 84 HOH HOH . G 4 HOH A 35 435 8 HOH HOH . G 4 HOH A 36 436 59 HOH HOH . G 4 HOH A 37 437 50 HOH HOH . G 4 HOH A 38 438 46 HOH HOH . G 4 HOH A 39 439 23 HOH HOH . G 4 HOH A 40 440 67 HOH HOH . G 4 HOH A 41 441 35 HOH HOH . G 4 HOH A 42 442 76 HOH HOH . G 4 HOH A 43 443 48 HOH HOH . G 4 HOH A 44 444 71 HOH HOH . G 4 HOH A 45 445 49 HOH HOH . G 4 HOH A 46 446 62 HOH HOH . G 4 HOH A 47 447 63 HOH HOH . G 4 HOH A 48 448 91 HOH HOH . G 4 HOH A 49 449 53 HOH HOH . G 4 HOH A 50 450 78 HOH HOH . G 4 HOH A 51 451 89 HOH HOH . G 4 HOH A 52 452 74 HOH HOH . G 4 HOH A 53 453 90 HOH HOH . G 4 HOH A 54 454 88 HOH HOH . H 4 HOH B 1 401 92 HOH HOH . H 4 HOH B 2 402 26 HOH HOH . H 4 HOH B 3 403 30 HOH HOH . H 4 HOH B 4 404 4 HOH HOH . H 4 HOH B 5 405 36 HOH HOH . H 4 HOH B 6 406 82 HOH HOH . H 4 HOH B 7 407 1 HOH HOH . H 4 HOH B 8 408 14 HOH HOH . H 4 HOH B 9 409 87 HOH HOH . H 4 HOH B 10 410 54 HOH HOH . H 4 HOH B 11 411 42 HOH HOH . H 4 HOH B 12 412 45 HOH HOH . H 4 HOH B 13 413 60 HOH HOH . H 4 HOH B 14 414 27 HOH HOH . H 4 HOH B 15 415 58 HOH HOH . H 4 HOH B 16 416 12 HOH HOH . H 4 HOH B 17 417 64 HOH HOH . H 4 HOH B 18 418 79 HOH HOH . H 4 HOH B 19 419 29 HOH HOH . H 4 HOH B 20 420 18 HOH HOH . H 4 HOH B 21 421 22 HOH HOH . H 4 HOH B 22 422 85 HOH HOH . H 4 HOH B 23 423 37 HOH HOH . H 4 HOH B 24 424 39 HOH HOH . H 4 HOH B 25 425 28 HOH HOH . H 4 HOH B 26 426 44 HOH HOH . H 4 HOH B 27 427 83 HOH HOH . H 4 HOH B 28 428 69 HOH HOH . H 4 HOH B 29 429 70 HOH HOH . H 4 HOH B 30 430 17 HOH HOH . H 4 HOH B 31 431 47 HOH HOH . H 4 HOH B 32 432 65 HOH HOH . H 4 HOH B 33 433 81 HOH HOH . H 4 HOH B 34 434 33 HOH HOH . H 4 HOH B 35 435 93 HOH HOH . H 4 HOH B 36 436 43 HOH HOH . H 4 HOH B 37 437 68 HOH HOH . H 4 HOH B 38 438 95 HOH HOH . H 4 HOH B 39 439 72 HOH HOH . H 4 HOH B 40 440 94 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 3 0.801 12.897 13.35 1 41.49 ? N SAH 302 A 1 HETATM 2 C CA SAH . . . D 3 -0.586 12.448 13.417 1 41.67 ? CA SAH 302 A 1 HETATM 3 C CB SAH . . . D 3 -0.719 11.007 12.936 1 41.79 ? CB SAH 302 A 1 HETATM 4 C CG SAH . . . D 3 0.052 10.632 11.674 1 42.27 ? CG SAH 302 A 1 HETATM 5 S SD SAH . . . D 3 -0.784 9.273 10.813 1 42.62 ? SD SAH 302 A 1 HETATM 6 C C SAH . . . D 3 -1.165 12.56 14.824 1 41.54 ? C SAH 302 A 1 HETATM 7 O O SAH . . . D 3 -0.687 13.331 15.652 1 40.82 ? O SAH 302 A 1 HETATM 8 O OXT SAH . . . D 3 -2.136 11.882 15.162 1 41.79 ? OXT SAH 302 A 1 HETATM 9 C C5' SAH . . . D 3 0.407 9.288 9.452 1 42.99 ? C5' SAH 302 A 1 HETATM 10 C C4' SAH . . . D 3 0.018 10.218 8.312 1 43.84 ? C4' SAH 302 A 1 HETATM 11 O O4' SAH . . . D 3 1.071 10.275 7.37 1 44.14 ? O4' SAH 302 A 1 HETATM 12 C C3' SAH . . . D 3 -1.215 9.73 7.566 1 44.81 ? C3' SAH 302 A 1 HETATM 13 O O3' SAH . . . D 3 -2.239 10.689 7.676 1 45.01 ? O3' SAH 302 A 1 HETATM 14 C C2' SAH . . . D 3 -0.794 9.613 6.116 1 45.28 ? C2' SAH 302 A 1 HETATM 15 O O2' SAH . . . D 3 -1.738 10.238 5.282 1 45.89 ? O2' SAH 302 A 1 HETATM 16 C C1' SAH . . . D 3 0.53 10.355 6.068 1 45.23 ? C1' SAH 302 A 1 HETATM 17 N N9 SAH . . . D 3 1.458 9.804 5.063 1 46.52 ? N9 SAH 302 A 1 HETATM 18 C C8 SAH . . . D 3 1.575 8.506 4.635 1 46.98 ? C8 SAH 302 A 1 HETATM 19 N N7 SAH . . . D 3 2.554 8.456 3.7 1 47.4 ? N7 SAH 302 A 1 HETATM 20 C C5 SAH . . . D 3 3.059 9.699 3.528 1 47.61 ? C5 SAH 302 A 1 HETATM 21 C C6 SAH . . . D 3 4.061 10.21 2.711 1 47.93 ? C6 SAH 302 A 1 HETATM 22 N N6 SAH . . . D 3 4.73 9.41 1.886 1 48.23 ? N6 SAH 302 A 1 HETATM 23 N N1 SAH . . . D 3 4.359 11.556 2.759 1 47.47 ? N1 SAH 302 A 1 HETATM 24 C C2 SAH . . . D 3 3.665 12.388 3.615 1 47.43 ? C2 SAH 302 A 1 HETATM 25 N N3 SAH . . . D 3 2.673 11.875 4.422 1 47.35 ? N3 SAH 302 A 1 HETATM 26 C C4 SAH . . . D 3 2.376 10.553 4.379 1 47.33 ? C4 SAH 302 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 26 #