data_6KR3 # _model_server_result.job_id 9AZE9sijyvMBRTrKv2Qk5w _model_server_result.datetime_utc '2025-08-28 04:42:58' _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":"X","auth_seq_id":1004}' # _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 . . . X 3 -85.166 -49.525 -27.224 0.9 52.37 ? N SAH 1004 B 1 HETATM 2 C CA SAH . . . X 3 -84.66 -50.889 -27.469 0.9 54.59 ? CA SAH 1004 B 1 HETATM 3 C CB SAH . . . X 3 -83.648 -51.35 -26.426 0.9 56.36 ? CB SAH 1004 B 1 HETATM 4 C CG SAH . . . X 3 -82.638 -50.313 -25.968 0.9 59.58 ? CG SAH 1004 B 1 HETATM 5 S SD SAH . . . X 3 -80.89 -50.643 -26.378 0.9 79.04 ? SD SAH 1004 B 1 HETATM 6 C C SAH . . . X 3 -85.753 -51.962 -27.654 0.9 74.62 ? C SAH 1004 B 1 HETATM 7 O O SAH . . . X 3 -85.458 -53.163 -27.473 0.9 79.01 ? O SAH 1004 B 1 HETATM 8 O OXT SAH . . . X 3 -86.925 -51.666 -28.013 0.9 69.36 ? OXT SAH 1004 B 1 HETATM 9 C C5' SAH . . . X 3 -80.939 -49.203 -27.483 0.9 58.6 ? C5' SAH 1004 B 1 HETATM 10 C C4' SAH . . . X 3 -80.222 -48.078 -26.754 0.9 64.49 ? C4' SAH 1004 B 1 HETATM 11 O O4' SAH . . . X 3 -78.91 -47.867 -27.249 0.9 71.63 ? O4' SAH 1004 B 1 HETATM 12 C C3' SAH . . . X 3 -80.868 -46.698 -26.776 0.9 64.13 ? C3' SAH 1004 B 1 HETATM 13 O O3' SAH . . . X 3 -81.599 -46.466 -25.586 0.9 58.76 ? O3' SAH 1004 B 1 HETATM 14 C C2' SAH . . . X 3 -79.666 -45.769 -26.728 0.9 62.38 ? C2' SAH 1004 B 1 HETATM 15 O O2' SAH . . . X 3 -79.846 -44.957 -25.59 0.9 63.95 ? O2' SAH 1004 B 1 HETATM 16 C C1' SAH . . . X 3 -78.457 -46.703 -26.596 0.9 64.8 ? C1' SAH 1004 B 1 HETATM 17 N N9 SAH . . . X 3 -77.163 -46.168 -27.137 0.9 65.49 ? N9 SAH 1004 B 1 HETATM 18 C C8 SAH . . . X 3 -76.22 -45.542 -26.353 0.9 64.06 ? C8 SAH 1004 B 1 HETATM 19 N N7 SAH . . . X 3 -75.154 -45.166 -27.129 0.9 73.98 ? N7 SAH 1004 B 1 HETATM 20 C C5 SAH . . . X 3 -75.398 -45.552 -28.409 0.9 71.63 ? C5 SAH 1004 B 1 HETATM 21 C C6 SAH . . . X 3 -74.64 -45.416 -29.593 0.9 67.93 ? C6 SAH 1004 B 1 HETATM 22 N N6 SAH . . . X 3 -73.456 -44.797 -29.528 0.9 63.26 ? N6 SAH 1004 B 1 HETATM 23 N N1 SAH . . . X 3 -75.121 -45.907 -30.795 0.9 71.99 ? N1 SAH 1004 B 1 HETATM 24 C C2 SAH . . . X 3 -76.366 -46.53 -30.804 0.9 71.26 ? C2 SAH 1004 B 1 HETATM 25 N N3 SAH . . . X 3 -77.119 -46.667 -29.631 0.9 74.42 ? N3 SAH 1004 B 1 HETATM 26 C C4 SAH . . . X 3 -76.658 -46.194 -28.436 0.9 68.11 ? C4 SAH 1004 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 55 _model_server_stats.query_time_ms 239 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #