data_8GZR # _model_server_result.job_id YJiaDzWPJVmt_J13rc2oZQ _model_server_result.datetime_utc '2024-10-20 03:47:07' _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 8gzr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1005}' # _entry.id 8GZR # _exptl.entry_id 8GZR _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 384.411 _entity.id 6 _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 8GZR _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GZR _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K _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 ? _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 6 _struct_asym.id H _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 OE2 GLU 445 A GLU 437 1_555 G ZN ZN . A ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc2 A NE2 HIS 449 A HIS 441 1_555 G ZN ZN . A ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc3 A SG CYS 454 A CYS 446 1_555 G ZN ZN . A ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc4 A SG CYS 457 A CYS 449 1_555 G ZN ZN . A ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc5 A OD1 ASP 541 A ASP 533 1_555 D MN MN . A MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.792 ? metalc ? metalc6 A OD2 ASP 541 A ASP 533 1_555 E MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.834 ? metalc ? metalc7 A O THR 542 A THR 534 1_555 D MN MN . A MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc8 A OD2 ASP 671 A ASP 663 1_555 D MN MN . A MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.897 ? metalc ? metalc9 A OD1 ASP 671 A ASP 663 1_555 E MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc10 A OD1 ASP 672 A ASP 664 1_555 E MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc11 A NE2 HIS 720 A HIS 712 1_555 F ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc12 A NE2 HIS 722 A HIS 714 1_555 F ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc13 A SG CYS 736 A CYS 728 1_555 F ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc14 A SG CYS 855 A CYS 847 1_555 F ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc15 D MN MN . A MN 1001 1_555 I O2A CDP . A CDP 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.664 ? metalc ? metalc16 D MN MN . A MN 1001 1_555 I O2B CDP . A CDP 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.733 ? metalc ? metalc17 E MN MN . A MN 1002 1_555 I O2A CDP . A CDP 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? metalc ? metalc18 B OG1 THR 255 B THR 201 1_555 J MN MN . B MN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc19 J MN MN . B MN 701 1_555 K O1B CDP . B CDP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.836 ? hydrog WATSON-CRICK hydrog1 C N1 A 17 C A 17 1_555 C N3 U 40 C U 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 C N6 A 17 C A 17 1_555 C O4 U 40 C U 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 C N1 A 18 C A 18 1_555 C N3 U 39 C U 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 C N6 A 18 C A 18 1_555 C O4 U 39 C U 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 C N3 C 19 C C 19 1_555 C N1 G 38 C G 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 C N4 C 19 C C 19 1_555 C O6 G 38 C G 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 C O2 C 19 C C 19 1_555 C N2 G 38 C G 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 C N1 A 20 C A 20 1_555 C N3 U 37 C U 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 C N6 A 20 C A 20 1_555 C O4 U 37 C U 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 C N1 G 21 C G 21 1_555 C N3 C 36 C C 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 C N2 G 21 C G 21 1_555 C O2 C 36 C C 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 C O6 G 21 C G 21 1_555 C N4 C 36 C C 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 C N1 G 22 C G 22 1_555 C N3 C 35 C C 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 C N2 G 22 C G 22 1_555 C O2 C 35 C C 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 C O6 G 22 C G 22 1_555 C N4 C 35 C C 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 C N3 U 23 C U 23 1_555 C N1 A 34 C A 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 C O4 U 23 C U 23 1_555 C N6 A 34 C A 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 C N3 U 24 C U 24 1_555 C N1 A 33 C A 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 C O4 U 24 C U 24 1_555 C N6 A 33 C A 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 C N3 C 25 C C 25 1_555 C N1 G 32 C G 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 C N4 C 25 C C 25 1_555 C O6 G 32 C G 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 C O2 C 25 C C 25 1_555 C N2 G 32 C G 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 C N3 U 26 C U 26 1_555 C N1 A 31 C A 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 C O4 U 26 C U 26 1_555 C N6 A 31 C A 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-A MISPAIR' hydrog25 C N2 G 27 C G 27 1_555 C N7 A 30 C A 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 431 n n N HN1 SAH sing 432 n n N HN2 SAH sing 433 n n CA CB SAH sing 434 n n CA C SAH sing 435 n n CA HA SAH sing 436 n n CB CG SAH sing 437 n n CB HB1 SAH sing 438 n n CB HB2 SAH sing 439 n n CG SD SAH sing 440 n n CG HG1 SAH sing 441 n n CG HG2 SAH sing 442 n n SD C5' SAH sing 443 n n C O SAH doub 444 n n C OXT SAH sing 445 n n OXT HXT SAH sing 446 n n C5' C4' SAH sing 447 n n C5' "H5'1" SAH sing 448 n n C5' "H5'2" SAH sing 449 n n C4' O4' SAH sing 450 n n C4' C3' SAH sing 451 n n C4' H4' SAH sing 452 n n O4' C1' SAH sing 453 n n C3' O3' SAH sing 454 n n C3' C2' SAH sing 455 n n C3' H3' SAH sing 456 n n O3' HO3' SAH sing 457 n n C2' O2' SAH sing 458 n n C2' C1' SAH sing 459 n n C2' H2' SAH sing 460 n n O2' HO2' SAH sing 461 n n C1' N9 SAH sing 462 n n C1' H1' SAH sing 463 n n N9 C8 SAH sing 464 n y N9 C4 SAH sing 465 n y C8 N7 SAH doub 466 n y C8 H8 SAH sing 467 n n N7 C5 SAH sing 468 n y C5 C6 SAH sing 469 n y C5 C4 SAH doub 470 n y C6 N6 SAH sing 471 n n C6 N1 SAH doub 472 n y N6 HN61 SAH sing 473 n n N6 HN62 SAH sing 474 n n N1 C2 SAH sing 475 n y C2 N3 SAH doub 476 n y C2 H2 SAH sing 477 n n N3 C4 SAH sing 478 n y # _atom_sites.entry_id 8GZR _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 D 4 MN A 1 1001 1 MN MN . E 4 MN A 1 1002 2 MN MN . F 5 ZN A 1 1003 4 ZN ZN . G 5 ZN A 1 1004 5 ZN ZN . H 6 SAH A 1 1005 6 SAH SAH . I 7 CDP A 1 1006 7 CDP CDP . J 4 MN B 1 701 3 MN MN . K 7 CDP B 1 702 8 CDP CDP . # 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 . . . H 6 108.398 100.898 126.463 1 59.46 ? N SAH 1005 A 1 HETATM 2 C CA SAH . . . H 6 109.486 100.681 127.428 1 59.46 ? CA SAH 1005 A 1 HETATM 3 C CB SAH . . . H 6 108.89 100.343 128.808 1 59.46 ? CB SAH 1005 A 1 HETATM 4 C CG SAH . . . H 6 108.598 101.59 129.631 1 59.46 ? CG SAH 1005 A 1 HETATM 5 S SD SAH . . . H 6 107.992 101.089 131.31 1 59.46 ? SD SAH 1005 A 1 HETATM 6 C C SAH . . . H 6 110.435 99.538 126.926 1 59.46 ? C SAH 1005 A 1 HETATM 7 O O SAH . . . H 6 110.08 98.882 125.931 1 59.46 ? O SAH 1005 A 1 HETATM 8 O OXT SAH . . . H 6 111.5 99.368 127.574 1 59.46 ? OXT SAH 1005 A 1 HETATM 9 C C5' SAH . . . H 6 107.555 102.598 132.247 1 59.46 ? C5' SAH 1005 A 1 HETATM 10 C C4' SAH . . . H 6 108.807 103.406 132.594 1 59.46 ? C4' SAH 1005 A 1 HETATM 11 O O4' SAH . . . H 6 108.479 104.753 132.857 1 59.46 ? O4' SAH 1005 A 1 HETATM 12 C C3' SAH . . . H 6 109.49 102.88 133.893 1 59.46 ? C3' SAH 1005 A 1 HETATM 13 O O3' SAH . . . H 6 110.744 102.387 133.566 1 59.46 ? O3' SAH 1005 A 1 HETATM 14 C C2' SAH . . . H 6 109.685 104.144 134.779 1 59.46 ? C2' SAH 1005 A 1 HETATM 15 O O2' SAH . . . H 6 111.032 104.285 135.056 1 59.46 ? O2' SAH 1005 A 1 HETATM 16 C C1' SAH . . . H 6 109.316 105.307 133.819 1 59.46 ? C1' SAH 1005 A 1 HETATM 17 N N9 SAH . . . H 6 108.591 106.383 134.531 1 59.46 ? N9 SAH 1005 A 1 HETATM 18 C C8 SAH . . . H 6 107.61 106.207 135.532 1 59.46 ? C8 SAH 1005 A 1 HETATM 19 N N7 SAH . . . H 6 107.119 107.358 136.002 1 59.46 ? N7 SAH 1005 A 1 HETATM 20 C C5 SAH . . . H 6 107.802 108.345 135.287 1 59.46 ? C5 SAH 1005 A 1 HETATM 21 C C6 SAH . . . H 6 107.724 109.755 135.333 1 59.46 ? C6 SAH 1005 A 1 HETATM 22 N N6 SAH . . . H 6 106.877 110.399 136.178 1 59.46 ? N6 SAH 1005 A 1 HETATM 23 N N1 SAH . . . H 6 108.517 110.509 134.512 1 59.46 ? N1 SAH 1005 A 1 HETATM 24 C C2 SAH . . . H 6 109.351 109.819 133.683 1 59.46 ? C2 SAH 1005 A 1 HETATM 25 N N3 SAH . . . H 6 109.528 108.491 133.532 1 59.46 ? N3 SAH 1005 A 1 HETATM 26 C C4 SAH . . . H 6 108.72 107.764 134.369 1 59.46 ? C4 SAH 1005 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 60 _model_server_stats.query_time_ms 348 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 26 #