data_8XQC # _model_server_result.job_id KyQx1BHmq4PlR1LYlksZRQ _model_server_result.datetime_utc '2025-04-01 14:55:01' _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 8xqc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1701}' # _entry.id 8XQC # _exptl.entry_id 8XQC _exptl.method 'ELECTRON MICROSCOPY' # _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 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 8XQC _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8XQC _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 _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 4 _struct_asym.id D _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 covale ? covale1 A CB CYS 881 A CYS 1226 1_555 C SG EIX 6 C EIX 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? covale ? covale2 B O3' DA 5 B DA 5 1_555 B P 5CM 6 B 5CM 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.602 ? covale ? covale3 B O3' 5CM 6 B 5CM 6 1_555 B P DG 7 B DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? covale ? covale4 C O3' DC 5 C DC 5 1_555 C P EIX 6 C EIX 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.607 ? covale ? covale5 C O3' EIX 6 C EIX 6 1_555 C P DG 7 C DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? metalc ? metalc1 A NE2 HIS 448 A HIS 793 1_555 F ZN ZN . A ZN 1703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc2 A SG CYS 475 A CYS 820 1_555 F ZN ZN . A ZN 1703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc3 A SG CYS 548 A CYS 893 1_555 F ZN ZN . A ZN 1703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc4 A SG CYS 551 A CYS 896 1_555 F ZN ZN . A ZN 1703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc5 A SG CYS 1131 A CYS 1476 1_555 E ZN ZN . A ZN 1702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc6 A SG CYS 1133 A CYS 1478 1_555 E ZN ZN . A ZN 1702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc7 A SG CYS 1140 A CYS 1485 1_555 E ZN ZN . A ZN 1702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc8 A NE2 HIS 1157 A HIS 1502 1_555 E ZN ZN . A ZN 1702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? hydrog WATSON-CRICK hydrog1 B N3 DC 2 B DC 2 1_555 C N1 DG 11 C DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 DC 2 B DC 2 1_555 C O6 DG 11 C DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 DC 2 B DC 2 1_555 C N2 DG 11 C DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DT 3 B DT 3 1_555 C N1 DA 10 C DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O4 DT 3 B DT 3 1_555 C N6 DA 10 C DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DT 4 B DT 4 1_555 C N1 DA 9 C DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B O4 DT 4 B DT 4 1_555 C N6 DA 9 C DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N1 DA 5 B DA 5 1_555 C N3 DT 8 C DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N6 DA 5 B DA 5 1_555 C O4 DT 8 C DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N3 5CM 6 B 5CM 6 1_555 C N1 DG 7 C DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N4 5CM 6 B 5CM 6 1_555 C O6 DG 7 C DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B O2 5CM 6 B 5CM 6 1_555 C N2 DG 7 C DG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog13 B N1 DA 9 B DA 9 1_555 C N3 DT 4 C DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N1 DA 10 B DA 10 1_555 C N3 DT 3 C DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N6 DA 10 B DA 10 1_555 C O4 DT 3 C DT 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N1 DG 11 B DG 11 1_555 C N3 DC 2 C DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N2 DG 11 B DG 11 1_555 C O2 DC 2 C DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O6 DG 11 B DG 11 1_555 C N4 DC 2 C DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N1 DG 12 B DG 12 1_555 C N3 DC 1 C DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N2 DG 12 B DG 12 1_555 C O2 DC 1 C DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B O6 DG 12 B DG 12 1_555 C N4 DC 1 C DC 1 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 . _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _chem_comp.type non-polymer _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 503 n n N HN1 SAH sing 504 n n N HN2 SAH sing 505 n n CA CB SAH sing 506 n n CA C SAH sing 507 n n CA HA SAH sing 508 n n CB CG SAH sing 509 n n CB HB1 SAH sing 510 n n CB HB2 SAH sing 511 n n CG SD SAH sing 512 n n CG HG1 SAH sing 513 n n CG HG2 SAH sing 514 n n SD C5' SAH sing 515 n n C O SAH doub 516 n n C OXT SAH sing 517 n n OXT HXT SAH sing 518 n n C5' C4' SAH sing 519 n n C5' "H5'1" SAH sing 520 n n C5' "H5'2" SAH sing 521 n n C4' O4' SAH sing 522 n n C4' C3' SAH sing 523 n n C4' H4' SAH sing 524 n n O4' C1' SAH sing 525 n n C3' O3' SAH sing 526 n n C3' C2' SAH sing 527 n n C3' H3' SAH sing 528 n n O3' HO3' SAH sing 529 n n C2' O2' SAH sing 530 n n C2' C1' SAH sing 531 n n C2' H2' SAH sing 532 n n O2' HO2' SAH sing 533 n n C1' N9 SAH sing 534 n n C1' H1' SAH sing 535 n n N9 C8 SAH sing 536 n y N9 C4 SAH sing 537 n y C8 N7 SAH doub 538 n y C8 H8 SAH sing 539 n n N7 C5 SAH sing 540 n y C5 C6 SAH sing 541 n y C5 C4 SAH doub 542 n y C6 N6 SAH sing 543 n n C6 N1 SAH doub 544 n y N6 HN61 SAH sing 545 n n N6 HN62 SAH sing 546 n n N1 C2 SAH sing 547 n y C2 N3 SAH doub 548 n y C2 H2 SAH sing 549 n n N3 C4 SAH sing 550 n y # _atom_sites.entry_id 8XQC _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 SAH A 1 1701 1 SAH SAH . E 5 ZN A 1 1702 1 ZN ZN . F 5 ZN A 1 1703 2 ZN ZN . # 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 4 162.503 130.356 141.544 0.67 88.07 ? N SAH 1701 A 1 HETATM 2 C CA SAH . . . D 4 163.49 130.687 140.53 0.67 88.82 ? CA SAH 1701 A 1 HETATM 3 C CB SAH . . . D 4 162.963 131.777 139.629 0.67 87.28 ? CB SAH 1701 A 1 HETATM 4 C CG SAH . . . D 4 162.288 131.247 138.379 0.67 89.16 ? CG SAH 1701 A 1 HETATM 5 S SD SAH . . . D 4 160.549 130.812 138.613 0.67 88.18 ? SD SAH 1701 A 1 HETATM 6 C C SAH . . . D 4 164.807 131.117 141.145 0.67 90.76 ? C SAH 1701 A 1 HETATM 7 O O SAH . . . D 4 165.319 132.21 140.915 0.67 90.64 ? O SAH 1701 A 1 HETATM 8 O OXT SAH . . . D 4 165.409 130.372 141.904 0.67 89.54 ? OXT SAH 1701 A 1 HETATM 9 C C5' SAH . . . D 4 160.165 132.104 137.411 0.67 87.97 ? C5' SAH 1701 A 1 HETATM 10 C C4' SAH . . . D 4 160.993 131.93 136.142 0.67 91.34 ? C4' SAH 1701 A 1 HETATM 11 O O4' SAH . . . D 4 160.76 130.672 135.543 0.67 93.27 ? O4' SAH 1701 A 1 HETATM 12 C C3' SAH . . . D 4 160.664 132.945 135.063 0.67 91.2 ? C3' SAH 1701 A 1 HETATM 13 O O3' SAH . . . D 4 161.568 134.02 135.116 0.67 90.76 ? O3' SAH 1701 A 1 HETATM 14 C C2' SAH . . . D 4 160.858 132.176 133.772 0.67 90.01 ? C2' SAH 1701 A 1 HETATM 15 O O2' SAH . . . D 4 161.931 132.724 133.046 0.67 89.15 ? O2' SAH 1701 A 1 HETATM 16 C C1' SAH . . . D 4 161.189 130.752 134.203 0.67 90.67 ? C1' SAH 1701 A 1 HETATM 17 N N9 SAH . . . D 4 160.463 129.782 133.372 0.67 90.77 ? N9 SAH 1701 A 1 HETATM 18 C C8 SAH . . . D 4 159.841 130.085 132.196 0.67 89.62 ? C8 SAH 1701 A 1 HETATM 19 N N7 SAH . . . D 4 159.296 128.952 131.71 0.67 91.75 ? N7 SAH 1701 A 1 HETATM 20 C C5 SAH . . . D 4 159.554 127.932 132.558 0.67 93.44 ? C5 SAH 1701 A 1 HETATM 21 C C6 SAH . . . D 4 159.218 126.581 132.525 0.67 92.8 ? C6 SAH 1701 A 1 HETATM 22 N N6 SAH . . . D 4 158.506 126.08 131.511 0.67 92.75 ? N6 SAH 1701 A 1 HETATM 23 N N1 SAH . . . D 4 159.639 125.769 133.558 0.67 89.23 ? N1 SAH 1701 A 1 HETATM 24 C C2 SAH . . . D 4 160.379 126.295 134.599 0.67 88.26 ? C2 SAH 1701 A 1 HETATM 25 N N3 SAH . . . D 4 160.695 127.635 134.626 0.67 89.69 ? N3 SAH 1701 A 1 HETATM 26 C C4 SAH . . . D 4 160.296 128.441 133.615 0.67 91.95 ? C4 SAH 1701 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #