data_5GM2 # _model_server_result.job_id 5Rky8NY0rGUL5uHy2Pt0BQ _model_server_result.datetime_utc '2025-03-01 19:11:23' _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 5gm2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"QA","auth_seq_id":301}' # _entry.id 5GM2 # _exptl.entry_id 5GM2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _entity.pdbx_number_of_molecules 18 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 93.06 _cell.angle_gamma 90 _cell.entry_id 5GM2 _cell.length_a 257.459 _cell.length_b 152.757 _cell.length_c 154.171 _cell.Z_PDB 72 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GM2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? hexameric 6 author_defined_assembly 1 ? hexameric 6 author_defined_assembly 2 ? hexameric 6 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,CB,DB,EB,FB,GB,HB 1 1 G,H,I,J,K,L,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,IB,JB,KB,LB,MB,NB 2 1 M,N,O,P,Q,R,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,OB,PB,QB,RB,SB,TB 3 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 ? 2 S N N ? 2 U N N ? 2 W N N ? 2 Y N N ? 2 AA N N ? 2 CA N N ? 2 EA N N ? 2 GA N N ? 2 IA N N ? 2 KA N N ? 2 MA N N ? 2 OA N N ? 2 QA N N ? 2 SA N N ? 2 UA N N ? 2 WA N N ? 2 YA N N ? 2 AB N N # _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 277 n n N HN1 SAH sing 278 n n N HN2 SAH sing 279 n n CA CB SAH sing 280 n n CA C SAH sing 281 n n CA HA SAH sing 282 n n CB CG SAH sing 283 n n CB HB1 SAH sing 284 n n CB HB2 SAH sing 285 n n CG SD SAH sing 286 n n CG HG1 SAH sing 287 n n CG HG2 SAH sing 288 n n SD C5' SAH sing 289 n n C O SAH doub 290 n n C OXT SAH sing 291 n n OXT HXT SAH sing 292 n n C5' C4' SAH sing 293 n n C5' "H5'1" SAH sing 294 n n C5' "H5'2" SAH sing 295 n n C4' O4' SAH sing 296 n n C4' C3' SAH sing 297 n n C4' H4' SAH sing 298 n n O4' C1' SAH sing 299 n n C3' O3' SAH sing 300 n n C3' C2' SAH sing 301 n n C3' H3' SAH sing 302 n n O3' HO3' SAH sing 303 n n C2' O2' SAH sing 304 n n C2' C1' SAH sing 305 n n C2' H2' SAH sing 306 n n O2' HO2' SAH sing 307 n n C1' N9 SAH sing 308 n n C1' H1' SAH sing 309 n n N9 C8 SAH sing 310 n y N9 C4 SAH sing 311 n y C8 N7 SAH doub 312 n y C8 H8 SAH sing 313 n n N7 C5 SAH sing 314 n y C5 C6 SAH sing 315 n y C5 C4 SAH doub 316 n y C6 N6 SAH sing 317 n n C6 N1 SAH doub 318 n y N6 HN61 SAH sing 319 n n N6 HN62 SAH sing 320 n n N1 C2 SAH sing 321 n y C2 N3 SAH doub 322 n y C2 H2 SAH sing 323 n n N3 C4 SAH sing 324 n y # _atom_sites.entry_id 5GM2 _atom_sites.fract_transf_matrix[1][1] 0.003884 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000208 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006546 _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] 0.006496 _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 S 2 SAH A 1 301 301 SAH SAH . T 3 TEX A 1 302 302 TEX TEL . U 2 SAH B 1 301 301 SAH SAH . V 3 TEX B 1 302 302 TEX TEL . W 2 SAH C 1 301 301 SAH SAH . X 3 TEX C 1 302 302 TEX TEL . Y 2 SAH D 1 301 301 SAH SAH . Z 3 TEX D 1 302 302 TEX TEL . AA 2 SAH E 1 301 301 SAH SAH . BA 3 TEX E 1 302 302 TEX TEL . CA 2 SAH F 1 301 301 SAH SAH . DA 3 TEX F 1 302 302 TEX TEL . EA 2 SAH G 1 301 301 SAH SAH . FA 3 TEX G 1 302 302 TEX TEL . GA 2 SAH H 1 301 301 SAH SAH . HA 3 TEX H 1 302 302 TEX TEL . IA 2 SAH I 1 301 301 SAH SAH . JA 3 TEX I 1 302 302 TEX TEL . KA 2 SAH J 1 301 301 SAH SAH . LA 3 TEX J 1 302 302 TEX TEL . MA 2 SAH K 1 301 301 SAH SAH . NA 3 TEX K 1 302 302 TEX TEL . OA 2 SAH L 1 301 301 SAH SAH . PA 3 TEX L 1 302 302 TEX TEL . QA 2 SAH M 1 301 301 SAH SAH . RA 3 TEX M 1 302 302 TEX TEL . SA 2 SAH N 1 301 301 SAH SAH . TA 3 TEX N 1 302 302 TEX TEL . UA 2 SAH O 1 301 301 SAH SAH . VA 3 TEX O 1 302 302 TEX TEL . WA 2 SAH P 1 301 301 SAH SAH . XA 3 TEX P 1 302 302 TEX TEL . YA 2 SAH Q 1 301 301 SAH SAH . ZA 3 TEX Q 1 302 302 TEX TEL . AB 2 SAH R 1 301 301 SAH SAH . BB 3 TEX R 1 302 302 TEX TEL . CB 4 HOH A 1 401 126 HOH HOH . CB 4 HOH A 2 402 38 HOH HOH . CB 4 HOH A 3 403 56 HOH HOH . CB 4 HOH A 4 404 2 HOH HOH . CB 4 HOH A 5 405 159 HOH HOH . CB 4 HOH A 6 406 76 HOH HOH . CB 4 HOH A 7 407 84 HOH HOH . CB 4 HOH A 8 408 27 HOH HOH . CB 4 HOH A 9 409 89 HOH HOH . CB 4 HOH A 10 410 31 HOH HOH . CB 4 HOH A 11 411 34 HOH HOH . CB 4 HOH A 12 412 30 HOH HOH . CB 4 HOH A 13 413 47 HOH HOH . CB 4 HOH A 14 414 74 HOH HOH . CB 4 HOH A 15 415 49 HOH HOH . CB 4 HOH A 16 416 75 HOH HOH . CB 4 HOH A 17 417 51 HOH HOH . CB 4 HOH A 18 418 28 HOH HOH . CB 4 HOH A 19 419 142 HOH HOH . CB 4 HOH A 20 420 131 HOH HOH . CB 4 HOH A 21 421 113 HOH HOH . DB 4 HOH B 1 401 21 HOH HOH . DB 4 HOH B 2 402 94 HOH HOH . DB 4 HOH B 3 403 166 HOH HOH . DB 4 HOH B 4 404 22 HOH HOH . DB 4 HOH B 5 405 158 HOH HOH . DB 4 HOH B 6 406 45 HOH HOH . DB 4 HOH B 7 407 71 HOH HOH . DB 4 HOH B 8 408 33 HOH HOH . DB 4 HOH B 9 409 59 HOH HOH . DB 4 HOH B 10 410 69 HOH HOH . DB 4 HOH B 11 411 95 HOH HOH . DB 4 HOH B 12 412 44 HOH HOH . DB 4 HOH B 13 413 6 HOH HOH . DB 4 HOH B 14 414 9 HOH HOH . DB 4 HOH B 15 415 90 HOH HOH . DB 4 HOH B 16 416 58 HOH HOH . DB 4 HOH B 17 417 83 HOH HOH . DB 4 HOH B 18 418 133 HOH HOH . DB 4 HOH B 19 419 103 HOH HOH . EB 4 HOH C 1 401 109 HOH HOH . EB 4 HOH C 2 402 79 HOH HOH . EB 4 HOH C 3 403 151 HOH HOH . EB 4 HOH C 4 404 117 HOH HOH . EB 4 HOH C 5 405 66 HOH HOH . EB 4 HOH C 6 406 149 HOH HOH . EB 4 HOH C 7 407 50 HOH HOH . EB 4 HOH C 8 408 102 HOH HOH . EB 4 HOH C 9 409 120 HOH HOH . FB 4 HOH D 1 401 14 HOH HOH . FB 4 HOH D 2 402 144 HOH HOH . FB 4 HOH D 3 403 62 HOH HOH . FB 4 HOH D 4 404 137 HOH HOH . FB 4 HOH D 5 405 29 HOH HOH . FB 4 HOH D 6 406 150 HOH HOH . FB 4 HOH D 7 407 124 HOH HOH . FB 4 HOH D 8 408 152 HOH HOH . FB 4 HOH D 9 409 118 HOH HOH . FB 4 HOH D 10 410 134 HOH HOH . FB 4 HOH D 11 411 136 HOH HOH . GB 4 HOH E 1 401 146 HOH HOH . GB 4 HOH E 2 402 115 HOH HOH . GB 4 HOH E 3 403 104 HOH HOH . GB 4 HOH E 4 404 24 HOH HOH . GB 4 HOH E 5 405 157 HOH HOH . GB 4 HOH E 6 406 80 HOH HOH . GB 4 HOH E 7 407 13 HOH HOH . GB 4 HOH E 8 408 39 HOH HOH . GB 4 HOH E 9 409 20 HOH HOH . GB 4 HOH E 10 410 26 HOH HOH . GB 4 HOH E 11 411 37 HOH HOH . GB 4 HOH E 12 412 132 HOH HOH . HB 4 HOH F 1 401 43 HOH HOH . HB 4 HOH F 2 402 140 HOH HOH . HB 4 HOH F 3 403 55 HOH HOH . HB 4 HOH F 4 404 145 HOH HOH . HB 4 HOH F 5 405 35 HOH HOH . HB 4 HOH F 6 406 101 HOH HOH . HB 4 HOH F 7 407 148 HOH HOH . HB 4 HOH F 8 408 93 HOH HOH . HB 4 HOH F 9 409 129 HOH HOH . HB 4 HOH F 10 410 15 HOH HOH . HB 4 HOH F 11 411 10 HOH HOH . HB 4 HOH F 12 412 64 HOH HOH . HB 4 HOH F 13 413 32 HOH HOH . HB 4 HOH F 14 414 1 HOH HOH . HB 4 HOH F 15 415 8 HOH HOH . HB 4 HOH F 16 416 36 HOH HOH . HB 4 HOH F 17 417 16 HOH HOH . HB 4 HOH F 18 418 163 HOH HOH . HB 4 HOH F 19 419 18 HOH HOH . HB 4 HOH F 20 420 114 HOH HOH . HB 4 HOH F 21 421 108 HOH HOH . HB 4 HOH F 22 422 63 HOH HOH . HB 4 HOH F 23 423 82 HOH HOH . HB 4 HOH F 24 424 70 HOH HOH . HB 4 HOH F 25 425 97 HOH HOH . HB 4 HOH F 26 426 153 HOH HOH . HB 4 HOH F 27 427 57 HOH HOH . HB 4 HOH F 28 428 46 HOH HOH . IB 4 HOH G 1 401 162 HOH HOH . IB 4 HOH G 2 402 112 HOH HOH . IB 4 HOH G 3 403 100 HOH HOH . IB 4 HOH G 4 404 41 HOH HOH . IB 4 HOH G 5 405 85 HOH HOH . IB 4 HOH G 6 406 164 HOH HOH . IB 4 HOH G 7 407 92 HOH HOH . JB 4 HOH H 1 401 160 HOH HOH . JB 4 HOH H 2 402 119 HOH HOH . JB 4 HOH H 3 403 147 HOH HOH . JB 4 HOH H 4 404 73 HOH HOH . KB 4 HOH I 1 401 4 HOH HOH . KB 4 HOH I 2 402 128 HOH HOH . KB 4 HOH I 3 403 68 HOH HOH . KB 4 HOH I 4 404 165 HOH HOH . KB 4 HOH I 5 405 121 HOH HOH . KB 4 HOH I 6 406 11 HOH HOH . KB 4 HOH I 7 407 91 HOH HOH . KB 4 HOH I 8 408 12 HOH HOH . KB 4 HOH I 9 409 77 HOH HOH . KB 4 HOH I 10 410 107 HOH HOH . KB 4 HOH I 11 411 19 HOH HOH . KB 4 HOH I 12 412 72 HOH HOH . KB 4 HOH I 13 413 86 HOH HOH . KB 4 HOH I 14 414 105 HOH HOH . LB 4 HOH J 1 401 106 HOH HOH . LB 4 HOH J 2 402 130 HOH HOH . MB 4 HOH K 1 401 99 HOH HOH . MB 4 HOH K 2 402 23 HOH HOH . MB 4 HOH K 3 403 53 HOH HOH . NB 4 HOH L 1 401 48 HOH HOH . NB 4 HOH L 2 402 161 HOH HOH . NB 4 HOH L 3 403 42 HOH HOH . OB 4 HOH M 1 401 87 HOH HOH . OB 4 HOH M 2 402 5 HOH HOH . OB 4 HOH M 3 403 52 HOH HOH . OB 4 HOH M 4 404 81 HOH HOH . OB 4 HOH M 5 405 116 HOH HOH . PB 4 HOH N 1 401 156 HOH HOH . PB 4 HOH N 2 402 61 HOH HOH . PB 4 HOH N 3 403 125 HOH HOH . PB 4 HOH N 4 404 155 HOH HOH . PB 4 HOH N 5 405 110 HOH HOH . QB 4 HOH O 1 401 25 HOH HOH . QB 4 HOH O 2 402 135 HOH HOH . QB 4 HOH O 3 403 123 HOH HOH . QB 4 HOH O 4 404 7 HOH HOH . QB 4 HOH O 5 405 111 HOH HOH . QB 4 HOH O 6 406 40 HOH HOH . QB 4 HOH O 7 407 65 HOH HOH . QB 4 HOH O 8 408 54 HOH HOH . RB 4 HOH P 1 401 154 HOH HOH . RB 4 HOH P 2 402 122 HOH HOH . SB 4 HOH Q 1 401 78 HOH HOH . SB 4 HOH Q 2 402 17 HOH HOH . TB 4 HOH R 1 401 3 HOH HOH . TB 4 HOH R 2 402 139 HOH HOH . TB 4 HOH R 3 403 143 HOH HOH . TB 4 HOH R 4 404 141 HOH HOH . TB 4 HOH R 5 405 60 HOH HOH . TB 4 HOH R 6 406 88 HOH HOH . TB 4 HOH R 7 407 67 HOH HOH . TB 4 HOH R 8 408 127 HOH HOH . TB 4 HOH R 9 409 138 HOH HOH . TB 4 HOH R 10 410 98 HOH HOH . TB 4 HOH R 11 411 96 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 . . . QA 2 -74.018 31.6 17.584 1 73.57 ? N SAH 301 M 1 HETATM 2 C CA SAH . . . QA 2 -74.531 32.499 18.614 1 73.63 ? CA SAH 301 M 1 HETATM 3 C CB SAH . . . QA 2 -74.2 33.949 18.281 1 73.45 ? CB SAH 301 M 1 HETATM 4 C CG SAH . . . QA 2 -74.229 34.295 16.798 1 74.4 ? CG SAH 301 M 1 HETATM 5 S SD SAH . . . QA 2 -73.906 36.058 16.542 1 76.36 ? SD SAH 301 M 1 HETATM 6 C C SAH . . . QA 2 -76.03 32.322 18.841 1 74.93 ? C SAH 301 M 1 HETATM 7 O O SAH . . . QA 2 -76.667 31.484 18.204 1 75.61 ? O SAH 301 M 1 HETATM 8 O OXT SAH . . . QA 2 -76.637 33.007 19.666 1 75.12 ? OXT SAH 301 M 1 HETATM 9 C C5' SAH . . . QA 2 -72.338 35.696 15.71 1 78.22 ? C5' SAH 301 M 1 HETATM 10 C C4' SAH . . . QA 2 -71.179 35.403 16.661 1 79.48 ? C4' SAH 301 M 1 HETATM 11 O O4' SAH . . . QA 2 -70.034 35.02 15.921 1 78.04 ? O4' SAH 301 M 1 HETATM 12 C C3' SAH . . . QA 2 -70.772 36.601 17.507 1 80.43 ? C3' SAH 301 M 1 HETATM 13 O O3' SAH . . . QA 2 -70.926 36.284 18.871 1 81.52 ? O3' SAH 301 M 1 HETATM 14 C C2' SAH . . . QA 2 -69.302 36.837 17.218 1 79.66 ? C2' SAH 301 M 1 HETATM 15 O O2' SAH . . . QA 2 -68.581 36.996 18.418 1 80.5 ? O2' SAH 301 M 1 HETATM 16 C C1' SAH . . . QA 2 -68.867 35.567 16.505 1 78.74 ? C1' SAH 301 M 1 HETATM 17 N N9 SAH . . . QA 2 -67.804 35.767 15.499 1 81.75 ? N9 SAH 301 M 1 HETATM 18 C C8 SAH . . . QA 2 -67.816 36.635 14.442 1 82.56 ? C8 SAH 301 M 1 HETATM 19 N N7 SAH . . . QA 2 -66.652 36.495 13.765 1 83.85 ? N7 SAH 301 M 1 HETATM 20 C C5 SAH . . . QA 2 -65.9 35.552 14.372 1 84.86 ? C5 SAH 301 M 1 HETATM 21 C C6 SAH . . . QA 2 -64.644 35.028 14.101 1 84.9 ? C6 SAH 301 M 1 HETATM 22 N N6 SAH . . . QA 2 -63.941 35.462 13.059 1 86.14 ? N6 SAH 301 M 1 HETATM 23 N N1 SAH . . . QA 2 -64.131 34.05 14.926 1 83.4 ? N1 SAH 301 M 1 HETATM 24 C C2 SAH . . . QA 2 -64.853 33.593 16.008 1 83.25 ? C2 SAH 301 M 1 HETATM 25 N N3 SAH . . . QA 2 -66.098 34.123 16.265 1 83.98 ? N3 SAH 301 M 1 HETATM 26 C C4 SAH . . . QA 2 -66.614 35.084 15.462 1 83.23 ? C4 SAH 301 M 1 # _model_server_stats.io_time_ms 396 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 60 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 26 #