data_8XE0 # _model_server_result.job_id pg2ZAKR97yaBrRoWXkZ4WA _model_server_result.datetime_utc '2024-12-12 00:00:59' _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 8xe0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":503}' # _entry.id 8XE0 # _exptl.entry_id 8XE0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 4 _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 8XE0 _cell.length_a 50.421 _cell.length_b 80.862 _cell.length_c 116.597 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8XE0 _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,I _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 ? 4 E N N ? 4 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 OD1 ASP 158 A ASP 155 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc2 A OD2 ASP 184 A ASP 181 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc3 A OD1 ASN 185 A ASN 182 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc4 C O3 H6N . A H6N 501 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.738 ? metalc ? metalc5 C O4 H6N . A H6N 501 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc6 D MG MG . A MG 502 1_555 H O HOH . A HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc7 B OD1 ASP 158 B ASP 155 1_555 F MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc8 B OD2 ASP 184 B ASP 181 1_555 F MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc9 B OD1 ASN 185 B ASN 182 1_555 F MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc10 F MG MG . B MG 301 1_555 I O HOH . B HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc11 F MG MG . B MG 301 1_555 I O HOH . B HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc12 F MG MG . B MG 301 1_555 I O HOH . B HOH 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? # _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 293 n n N HN1 SAH sing 294 n n N HN2 SAH sing 295 n n CA CB SAH sing 296 n n CA C SAH sing 297 n n CA HA SAH sing 298 n n CB CG SAH sing 299 n n CB HB1 SAH sing 300 n n CB HB2 SAH sing 301 n n CG SD SAH sing 302 n n CG HG1 SAH sing 303 n n CG HG2 SAH sing 304 n n SD C5' SAH sing 305 n n C O SAH doub 306 n n C OXT SAH sing 307 n n OXT HXT SAH sing 308 n n C5' C4' SAH sing 309 n n C5' "H5'1" SAH sing 310 n n C5' "H5'2" SAH sing 311 n n C4' O4' SAH sing 312 n n C4' C3' SAH sing 313 n n C4' H4' SAH sing 314 n n O4' C1' SAH sing 315 n n C3' O3' SAH sing 316 n n C3' C2' SAH sing 317 n n C3' H3' SAH sing 318 n n O3' HO3' SAH sing 319 n n C2' O2' SAH sing 320 n n C2' C1' SAH sing 321 n n C2' H2' SAH sing 322 n n O2' HO2' SAH sing 323 n n C1' N9 SAH sing 324 n n C1' H1' SAH sing 325 n n N9 C8 SAH sing 326 n y N9 C4 SAH sing 327 n y C8 N7 SAH doub 328 n y C8 H8 SAH sing 329 n n N7 C5 SAH sing 330 n y C5 C6 SAH sing 331 n y C5 C4 SAH doub 332 n y C6 N6 SAH sing 333 n n C6 N1 SAH doub 334 n y N6 HN61 SAH sing 335 n n N6 HN62 SAH sing 336 n n N1 C2 SAH sing 337 n y C2 N3 SAH doub 338 n y C2 H2 SAH sing 339 n n N3 C4 SAH sing 340 n y # _atom_sites.entry_id 8XE0 _atom_sites.fract_transf_matrix[1][1] 0.019833 _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] 0.012367 _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] 0.008577 _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 H6N A 1 501 501 H6N LIG . D 3 MG A 1 502 301 MG MG . E 4 SAH A 1 503 401 SAH SAH . F 3 MG B 1 301 301 MG MG . G 4 SAH B 1 302 401 SAH SAH . H 5 HOH A 1 601 14 HOH HOH . H 5 HOH A 2 602 34 HOH HOH . H 5 HOH A 3 603 38 HOH HOH . H 5 HOH A 4 604 32 HOH HOH . H 5 HOH A 5 605 71 HOH HOH . H 5 HOH A 6 606 28 HOH HOH . H 5 HOH A 7 607 15 HOH HOH . H 5 HOH A 8 608 5 HOH HOH . H 5 HOH A 9 609 51 HOH HOH . H 5 HOH A 10 610 3 HOH HOH . H 5 HOH A 11 611 60 HOH HOH . H 5 HOH A 12 612 2 HOH HOH . H 5 HOH A 13 613 52 HOH HOH . H 5 HOH A 14 614 16 HOH HOH . H 5 HOH A 15 615 73 HOH HOH . H 5 HOH A 16 616 58 HOH HOH . H 5 HOH A 17 617 49 HOH HOH . H 5 HOH A 18 618 8 HOH HOH . H 5 HOH A 19 619 45 HOH HOH . H 5 HOH A 20 620 11 HOH HOH . H 5 HOH A 21 621 44 HOH HOH . H 5 HOH A 22 622 39 HOH HOH . H 5 HOH A 23 623 41 HOH HOH . H 5 HOH A 24 624 35 HOH HOH . H 5 HOH A 25 625 13 HOH HOH . H 5 HOH A 26 626 55 HOH HOH . H 5 HOH A 27 627 30 HOH HOH . H 5 HOH A 28 628 59 HOH HOH . H 5 HOH A 29 629 27 HOH HOH . H 5 HOH A 30 630 21 HOH HOH . H 5 HOH A 31 631 63 HOH HOH . H 5 HOH A 32 632 78 HOH HOH . H 5 HOH A 33 633 80 HOH HOH . H 5 HOH A 34 634 31 HOH HOH . H 5 HOH A 35 635 79 HOH HOH . H 5 HOH A 36 636 48 HOH HOH . H 5 HOH A 37 637 82 HOH HOH . I 5 HOH B 1 401 64 HOH HOH . I 5 HOH B 2 402 1 HOH HOH . I 5 HOH B 3 403 37 HOH HOH . I 5 HOH B 4 404 17 HOH HOH . I 5 HOH B 5 405 67 HOH HOH . I 5 HOH B 6 406 42 HOH HOH . I 5 HOH B 7 407 10 HOH HOH . I 5 HOH B 8 408 70 HOH HOH . I 5 HOH B 9 409 24 HOH HOH . I 5 HOH B 10 410 19 HOH HOH . I 5 HOH B 11 411 61 HOH HOH . I 5 HOH B 12 412 26 HOH HOH . I 5 HOH B 13 413 33 HOH HOH . I 5 HOH B 14 414 18 HOH HOH . I 5 HOH B 15 415 76 HOH HOH . I 5 HOH B 16 416 12 HOH HOH . I 5 HOH B 17 417 53 HOH HOH . I 5 HOH B 18 418 40 HOH HOH . I 5 HOH B 19 419 57 HOH HOH . I 5 HOH B 20 420 50 HOH HOH . I 5 HOH B 21 421 6 HOH HOH . I 5 HOH B 22 422 43 HOH HOH . I 5 HOH B 23 423 4 HOH HOH . I 5 HOH B 24 424 65 HOH HOH . I 5 HOH B 25 425 47 HOH HOH . I 5 HOH B 26 426 9 HOH HOH . I 5 HOH B 27 427 77 HOH HOH . I 5 HOH B 28 428 68 HOH HOH . I 5 HOH B 29 429 7 HOH HOH . I 5 HOH B 30 430 22 HOH HOH . I 5 HOH B 31 431 25 HOH HOH . I 5 HOH B 32 432 56 HOH HOH . I 5 HOH B 33 433 69 HOH HOH . I 5 HOH B 34 434 85 HOH HOH . I 5 HOH B 35 435 23 HOH HOH . I 5 HOH B 36 436 46 HOH HOH . I 5 HOH B 37 437 36 HOH HOH . I 5 HOH B 38 438 66 HOH HOH . I 5 HOH B 39 439 74 HOH HOH . I 5 HOH B 40 440 20 HOH HOH . I 5 HOH B 41 441 83 HOH HOH . I 5 HOH B 42 442 75 HOH HOH . I 5 HOH B 43 443 72 HOH HOH . I 5 HOH B 44 444 84 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 . . . E 4 0.571 13.159 13.345 1 41.92 ? N SAH 503 A 1 HETATM 2 C CA SAH . . . E 4 -0.766 12.582 13.434 1 42.84 ? CA SAH 503 A 1 HETATM 3 C CB SAH . . . E 4 -0.737 11.103 13.056 1 39.13 ? CB SAH 503 A 1 HETATM 4 C CG SAH . . . E 4 -0.044 10.756 11.739 1 45.65 ? CG SAH 503 A 1 HETATM 5 S SD SAH . . . E 4 -0.892 9.384 10.907 1 43.43 ? SD SAH 503 A 1 HETATM 6 C C SAH . . . E 4 -1.379 12.754 14.825 1 43.4 ? C SAH 503 A 1 HETATM 7 O O SAH . . . E 4 -0.988 13.631 15.595 1 40.88 ? O SAH 503 A 1 HETATM 8 O OXT SAH . . . E 4 -2.294 12.024 15.21 1 44.74 ? OXT SAH 503 A 1 HETATM 9 C C5' SAH . . . E 4 0.294 9.334 9.538 1 42.25 ? C5' SAH 503 A 1 HETATM 10 C C4' SAH . . . E 4 -0.016 10.308 8.404 1 47.49 ? C4' SAH 503 A 1 HETATM 11 O O4' SAH . . . E 4 1.058 10.342 7.482 1 44.07 ? O4' SAH 503 A 1 HETATM 12 C C3' SAH . . . E 4 -1.253 9.908 7.613 1 52.93 ? C3' SAH 503 A 1 HETATM 13 O O3' SAH . . . E 4 -2.197 10.951 7.676 1 54.09 ? O3' SAH 503 A 1 HETATM 14 C C2' SAH . . . E 4 -0.785 9.744 6.18 1 48.72 ? C2' SAH 503 A 1 HETATM 15 O O2' SAH . . . E 4 -1.694 10.345 5.289 1 49.21 ? O2' SAH 503 A 1 HETATM 16 C C1' SAH . . . E 4 0.545 10.477 6.171 1 45.13 ? C1' SAH 503 A 1 HETATM 17 N N9 SAH . . . E 4 1.493 9.974 5.157 1 50.42 ? N9 SAH 503 A 1 HETATM 18 C C8 SAH . . . E 4 1.656 8.687 4.711 1 50.22 ? C8 SAH 503 A 1 HETATM 19 N N7 SAH . . . E 4 2.638 8.681 3.777 1 49.44 ? N7 SAH 503 A 1 HETATM 20 C C5 SAH . . . E 4 3.101 9.943 3.623 1 56.02 ? C5 SAH 503 A 1 HETATM 21 C C6 SAH . . . E 4 4.088 10.494 2.812 1 54.99 ? C6 SAH 503 A 1 HETATM 22 N N6 SAH . . . E 4 4.781 9.723 1.98 1 57.17 ? N6 SAH 503 A 1 HETATM 23 N N1 SAH . . . E 4 4.343 11.849 2.874 1 50.74 ? N1 SAH 503 A 1 HETATM 24 C C2 SAH . . . E 4 3.622 12.647 3.739 1 48.68 ? C2 SAH 503 A 1 HETATM 25 N N3 SAH . . . E 4 2.645 12.093 4.541 1 46.48 ? N3 SAH 503 A 1 HETATM 26 C C4 SAH . . . E 4 2.388 10.764 4.484 1 49.71 ? C4 SAH 503 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 242 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 26 #