data_6KR3 # _model_server_result.job_id 9JueaXYoRMr87I8Vqd5SBQ _model_server_result.datetime_utc '2025-08-28 04:44:56' _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 6kr3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":1005}' # _entry.id 6KR3 # _exptl.entry_id 6KR3 _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 4 _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 6KR3 _cell.length_a 178.845 _cell.length_b 209.975 _cell.length_c 157.873 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KR3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,EA 1 1 B,U,V,W,X,Y,Z,AA,BA,CA,DA,FA 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 ? 3 O N N ? 3 P N N ? 3 X N N ? 3 Y 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 NE2 HIS 443 A HIS 442 1_555 Q ZN ZN . A ZN 1015 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc2 A SG CYS 448 A CYS 447 1_555 Q ZN ZN . A ZN 1015 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc3 A SG CYS 451 A CYS 450 1_555 Q ZN ZN . A ZN 1015 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? metalc ? metalc4 A NE2 HIS 713 A HIS 712 1_555 R ZN ZN . A ZN 1016 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.761 ? metalc ? metalc5 A NE2 HIS 715 A HIS 714 1_555 R ZN ZN . A ZN 1016 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc6 A SG CYS 729 A CYS 728 1_555 R ZN ZN . A ZN 1016 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc7 A SG CYS 848 A CYS 847 1_555 R ZN ZN . A ZN 1016 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.925 ? metalc ? metalc8 B NE2 HIS 443 B HIS 442 1_555 Z ZN ZN . B ZN 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc9 B SG CYS 451 B CYS 450 1_555 Z ZN ZN . B ZN 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc10 B NE2 HIS 713 B HIS 712 1_555 AA ZN ZN . B ZN 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.741 ? metalc ? metalc11 B NE2 HIS 715 B HIS 714 1_555 AA ZN ZN . B ZN 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.76 ? metalc ? metalc12 B SG CYS 729 B CYS 728 1_555 AA ZN ZN . B ZN 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc13 B SG CYS 848 B CYS 847 1_555 AA ZN ZN . B ZN 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? # _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 290 n n N HN1 SAH sing 291 n n N HN2 SAH sing 292 n n CA CB SAH sing 293 n n CA C SAH sing 294 n n CA HA SAH sing 295 n n CB CG SAH sing 296 n n CB HB1 SAH sing 297 n n CB HB2 SAH sing 298 n n CG SD SAH sing 299 n n CG HG1 SAH sing 300 n n CG HG2 SAH sing 301 n n SD C5' SAH sing 302 n n C O SAH doub 303 n n C OXT SAH sing 304 n n OXT HXT SAH sing 305 n n C5' C4' SAH sing 306 n n C5' "H5'1" SAH sing 307 n n C5' "H5'2" SAH sing 308 n n C4' O4' SAH sing 309 n n C4' C3' SAH sing 310 n n C4' H4' SAH sing 311 n n O4' C1' SAH sing 312 n n C3' O3' SAH sing 313 n n C3' C2' SAH sing 314 n n C3' H3' SAH sing 315 n n O3' HO3' SAH sing 316 n n C2' O2' SAH sing 317 n n C2' C1' SAH sing 318 n n C2' H2' SAH sing 319 n n O2' HO2' SAH sing 320 n n C1' N9 SAH sing 321 n n C1' H1' SAH sing 322 n n N9 C8 SAH sing 323 n y N9 C4 SAH sing 324 n y C8 N7 SAH doub 325 n y C8 H8 SAH sing 326 n n N7 C5 SAH sing 327 n y C5 C6 SAH sing 328 n y C5 C4 SAH doub 329 n y C6 N6 SAH sing 330 n n C6 N1 SAH doub 331 n y N6 HN61 SAH sing 332 n n N6 HN62 SAH sing 333 n n N1 C2 SAH sing 334 n y C2 N3 SAH doub 335 n y C2 H2 SAH sing 336 n n N3 C4 SAH sing 337 n y # _atom_sites.entry_id 6KR3 _atom_sites.fract_transf_matrix[1][1] 0.005591 _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] 0.004762 _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] 0.006334 _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 IOD A 1 1001 501 IOD IOD . D 2 IOD A 1 1002 502 IOD IOD . E 2 IOD A 1 1003 503 IOD IOD . F 2 IOD A 1 1004 504 IOD IOD . G 2 IOD A 1 1005 505 IOD IOD . H 2 IOD A 1 1006 506 IOD IOD . I 2 IOD A 1 1007 509 IOD IOD . J 2 IOD A 1 1008 510 IOD IOD . K 2 IOD A 1 1009 512 IOD IOD . L 2 IOD A 1 1010 517 IOD IOD . M 2 IOD A 1 1011 518 IOD IOD . N 2 IOD A 1 1012 520 IOD IOD . O 3 SAH A 1 1013 1001 SAH SAH . P 3 SAH A 1 1014 1011 SAH SAH . Q 4 ZN A 1 1015 2001 ZN ZN . R 4 ZN A 1 1016 2002 ZN ZN . S 5 GOL A 1 1017 128 GOL GOL . T 5 GOL A 1 1018 129 GOL GOL . U 2 IOD B 1 1001 507 IOD IOD . V 2 IOD B 1 1002 508 IOD IOD . W 2 IOD B 1 1003 514 IOD IOD . X 3 SAH B 1 1004 1031 SAH SAH . Y 3 SAH B 1 1005 1041 SAH SAH . Z 4 ZN B 1 1006 2003 ZN ZN . AA 4 ZN B 1 1007 2004 ZN ZN . BA 5 GOL B 1 1008 125 GOL GOL . CA 5 GOL B 1 1009 126 GOL GOL . DA 5 GOL B 1 1010 130 GOL GOL . EA 6 HOH A 1 1101 5 HOH HOH . EA 6 HOH A 2 1102 10 HOH HOH . EA 6 HOH A 3 1103 46 HOH HOH . EA 6 HOH A 4 1104 16 HOH HOH . EA 6 HOH A 5 1105 7 HOH HOH . EA 6 HOH A 6 1106 44 HOH HOH . EA 6 HOH A 7 1107 9 HOH HOH . EA 6 HOH A 8 1108 34 HOH HOH . EA 6 HOH A 9 1109 42 HOH HOH . EA 6 HOH A 10 1110 45 HOH HOH . EA 6 HOH A 11 1111 3 HOH HOH . EA 6 HOH A 12 1112 14 HOH HOH . EA 6 HOH A 13 1113 4 HOH HOH . EA 6 HOH A 14 1114 15 HOH HOH . EA 6 HOH A 15 1115 43 HOH HOH . EA 6 HOH A 16 1116 41 HOH HOH . EA 6 HOH A 17 1117 39 HOH HOH . EA 6 HOH A 18 1118 32 HOH HOH . EA 6 HOH A 19 1119 47 HOH HOH . EA 6 HOH A 20 1120 2 HOH HOH . EA 6 HOH A 21 1121 6 HOH HOH . EA 6 HOH A 22 1122 18 HOH HOH . EA 6 HOH A 23 1123 31 HOH HOH . EA 6 HOH A 24 1124 13 HOH HOH . EA 6 HOH A 25 1125 49 HOH HOH . EA 6 HOH A 26 1126 17 HOH HOH . EA 6 HOH A 27 1127 11 HOH HOH . EA 6 HOH A 28 1128 38 HOH HOH . EA 6 HOH A 29 1129 35 HOH HOH . EA 6 HOH A 30 1130 37 HOH HOH . EA 6 HOH A 31 1131 36 HOH HOH . FA 6 HOH B 1 1101 27 HOH HOH . FA 6 HOH B 2 1102 40 HOH HOH . FA 6 HOH B 3 1103 28 HOH HOH . FA 6 HOH B 4 1104 19 HOH HOH . FA 6 HOH B 5 1105 1 HOH HOH . FA 6 HOH B 6 1106 24 HOH HOH . FA 6 HOH B 7 1107 8 HOH HOH . FA 6 HOH B 8 1108 22 HOH HOH . FA 6 HOH B 9 1109 51 HOH HOH . FA 6 HOH B 10 1110 50 HOH HOH . FA 6 HOH B 11 1111 29 HOH HOH . FA 6 HOH B 12 1112 26 HOH HOH . FA 6 HOH B 13 1113 23 HOH HOH . FA 6 HOH B 14 1114 30 HOH HOH . FA 6 HOH B 15 1115 25 HOH HOH . FA 6 HOH B 16 1116 21 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 . . . Y 3 -83.473 -63.232 -8.547 0.85 78.2 ? N SAH 1005 B 1 HETATM 2 C CA SAH . . . Y 3 -82.692 -62.792 -7.375 0.85 76.8 ? CA SAH 1005 B 1 HETATM 3 C CB SAH . . . Y 3 -81.229 -63.282 -7.402 0.85 72.8 ? CB SAH 1005 B 1 HETATM 4 C CG SAH . . . Y 3 -80.831 -64.452 -6.478 0.85 74.45 ? CG SAH 1005 B 1 HETATM 5 S SD SAH . . . Y 3 -79.413 -65.458 -7.032 0.85 90.42 ? SD SAH 1005 B 1 HETATM 6 C C SAH . . . Y 3 -82.653 -61.271 -7.276 0.85 81.7 ? C SAH 1005 B 1 HETATM 7 O O SAH . . . Y 3 -82.474 -60.708 -6.167 0.85 81.83 ? O SAH 1005 B 1 HETATM 8 O OXT SAH . . . Y 3 -82.777 -60.599 -8.312 0.85 83.83 ? OXT SAH 1005 B 1 HETATM 9 C C5' SAH . . . Y 3 -80.545 -66.832 -7.332 0.85 76.57 ? C5' SAH 1005 B 1 HETATM 10 C C4' SAH . . . Y 3 -81.052 -67.368 -5.988 0.85 77.8 ? C4' SAH 1005 B 1 HETATM 11 O O4' SAH . . . Y 3 -81.819 -68.551 -6.167 0.85 79.44 ? O4' SAH 1005 B 1 HETATM 12 C C3' SAH . . . Y 3 -79.944 -67.723 -4.981 0.85 72.73 ? C3' SAH 1005 B 1 HETATM 13 O O3' SAH . . . Y 3 -79.978 -66.798 -3.912 0.85 81.28 ? O3' SAH 1005 B 1 HETATM 14 C C2' SAH . . . Y 3 -80.278 -69.119 -4.447 0.85 78.25 ? C2' SAH 1005 B 1 HETATM 15 O O2' SAH . . . Y 3 -80.566 -69.114 -3.062 0.85 89.52 ? O2' SAH 1005 B 1 HETATM 16 C C1' SAH . . . Y 3 -81.586 -69.483 -5.124 0.85 79.07 ? C1' SAH 1005 B 1 HETATM 17 N N9 SAH . . . Y 3 -81.504 -70.784 -5.789 0.85 78.8 ? N9 SAH 1005 B 1 HETATM 18 C C8 SAH . . . Y 3 -80.352 -71.365 -6.265 0.85 75.95 ? C8 SAH 1005 B 1 HETATM 19 N N7 SAH . . . Y 3 -80.687 -72.539 -6.857 0.85 74.18 ? N7 SAH 1005 B 1 HETATM 20 C C5 SAH . . . Y 3 -82.029 -72.68 -6.75 0.85 76.05 ? C5 SAH 1005 B 1 HETATM 21 C C6 SAH . . . Y 3 -82.835 -73.704 -7.192 0.85 84.12 ? C6 SAH 1005 B 1 HETATM 22 N N6 SAH . . . Y 3 -82.184 -74.719 -7.795 0.85 81.5 ? N6 SAH 1005 B 1 HETATM 23 N N1 SAH . . . Y 3 -84.198 -73.606 -6.957 0.85 83.65 ? N1 SAH 1005 B 1 HETATM 24 C C2 SAH . . . Y 3 -84.73 -72.505 -6.291 0.85 82.09 ? C2 SAH 1005 B 1 HETATM 25 N N3 SAH . . . Y 3 -83.909 -71.49 -5.858 0.85 84.44 ? N3 SAH 1005 B 1 HETATM 26 C C4 SAH . . . Y 3 -82.581 -71.582 -6.074 0.85 77.71 ? C4 SAH 1005 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 242 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 26 #