data_8XNR # _model_server_result.job_id sJIEKc3aBBEpoJlV5ul_DQ _model_server_result.datetime_utc '2025-06-22 17:15:52' _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 8xnr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"OA","auth_seq_id":201}' # _entry.id 8XNR # _exptl.entry_id 8XNR _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 584.703 _entity.id 33 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 23-meric _pdbx_struct_assembly.oligomeric_count 23 _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,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA _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 33 _struct_asym.id OA _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 disulf ? disulf1 M SG CYS 24 S CYS 24 1_555 M SG CYS 58 S CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 Q SG CYS 46 X CYS 46 1_555 Q SG CYS 56 X CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 Q SG CYS 88 X CYS 88 1_555 Q SG CYS 100 X CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc1 B SG CYS 99 B CYS 99 1_555 Y FE1 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc2 B SG CYS 194 B CYS 194 1_555 Y FE3 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc3 E SG CYS 134 E CYS 134 1_555 BA FE1 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc4 E SG CYS 175 E CYS 175 1_555 BA FE2 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? metalc ? metalc5 F SG CYS 385 F CYS 385 1_555 DA FE2 SF4 . F SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.551 ? metalc ? metalc6 G O PHE 63 G PHE 63 1_555 GA FE1 FES . G FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc7 G SG CYS 75 G CYS 75 1_555 GA FE1 FES . G FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc8 G NE2 HIS 124 G HIS 124 1_555 EA FE1 SF4 . G SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? metalc ? metalc9 G SG CYS 128 G CYS 128 1_555 EA FE3 SF4 . G SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc10 G SG CYS 137 G CYS 137 1_555 EA FE4 SF4 . G SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc11 G SG CYS 182 G CYS 182 1_555 FA FE2 SF4 . G SF4 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc12 I SG CYS 116 I CYS 116 1_555 LA FE1 SF4 . I SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc13 I SG CYS 119 I CYS 119 1_555 LA FE2 SF4 . I SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc14 I SG CYS 158 I CYS 158 1_555 KA FE3 SF4 . I SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc15 L SG CYS 79 R CYS 79 1_555 NA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc16 L NE2 HIS 88 R HIS 88 1_555 NA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc17 L SG CYS 104 R CYS 104 1_555 NA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc18 L SG CYS 107 R CYS 107 1_555 NA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? # _chem_comp.formula 'C25 H49 N2 O9 P S' _chem_comp.formula_weight 584.703 _chem_comp.id EHZ _chem_comp.mon_nstd_flag . _chem_comp.name '~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate' _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 O7 P1 EHZ sing 215 n n O9 P1 EHZ doub 216 n n P1 O6 EHZ sing 217 n n O6 C20 EHZ sing 218 n n C20 C17 EHZ sing 219 n n O5 C16 EHZ sing 220 n n C19 C17 EHZ sing 221 n n C17 C16 EHZ sing 222 n n C17 C18 EHZ sing 223 n n C16 C15 EHZ sing 224 n n C15 O4 EHZ doub 225 n n C15 N2 EHZ sing 226 n n N2 C14 EHZ sing 227 n n C13 C14 EHZ sing 228 n n C13 C12 EHZ sing 229 n n N1 C12 EHZ sing 230 n n N1 C11 EHZ sing 231 n n C12 O3 EHZ doub 232 n n C11 C10 EHZ sing 233 n n O2 C9 EHZ doub 234 n n C10 S1 EHZ sing 235 n n C7 C6 EHZ sing 236 n n C7 C8 EHZ sing 237 n n C7 O1 EHZ sing 238 n n C9 S1 EHZ sing 239 n n C9 C8 EHZ sing 240 n n C6 C5 EHZ sing 241 n n C22 C21 EHZ sing 242 n n C1 C21 EHZ sing 243 n n C1 C2 EHZ sing 244 n n C3 C2 EHZ sing 245 n n C3 C4 EHZ sing 246 n n C5 C4 EHZ sing 247 n n O1 H1 EHZ sing 248 n n C1 H2 EHZ sing 249 n n C1 H3 EHZ sing 250 n n C2 H4 EHZ sing 251 n n C2 H5 EHZ sing 252 n n C3 H6 EHZ sing 253 n n C3 H7 EHZ sing 254 n n C4 H8 EHZ sing 255 n n C4 H9 EHZ sing 256 n n C5 H10 EHZ sing 257 n n C5 H11 EHZ sing 258 n n C6 H12 EHZ sing 259 n n C6 H13 EHZ sing 260 n n C7 H14 EHZ sing 261 n n C8 H15 EHZ sing 262 n n C8 H16 EHZ sing 263 n n C10 H17 EHZ sing 264 n n C10 H18 EHZ sing 265 n n C11 H19 EHZ sing 266 n n C11 H20 EHZ sing 267 n n C13 H21 EHZ sing 268 n n C13 H22 EHZ sing 269 n n C14 H23 EHZ sing 270 n n C14 H24 EHZ sing 271 n n C16 H25 EHZ sing 272 n n C18 H26 EHZ sing 273 n n C18 H27 EHZ sing 274 n n C18 H28 EHZ sing 275 n n C19 H29 EHZ sing 276 n n C19 H30 EHZ sing 277 n n C19 H31 EHZ sing 278 n n C20 H32 EHZ sing 279 n n C20 H33 EHZ sing 280 n n C21 H34 EHZ sing 281 n n C21 H35 EHZ sing 282 n n C22 H36 EHZ sing 283 n n C22 H37 EHZ sing 284 n n N1 H39 EHZ sing 285 n n N2 H40 EHZ sing 286 n n O5 H41 EHZ sing 287 n n O7 H42 EHZ sing 288 n n P1 OP3 EHZ sing 289 n n C22 C23 EHZ sing 290 n n C23 C24 EHZ sing 291 n n C24 C25 EHZ sing 292 n n OP3 H44 EHZ sing 293 n n C23 H45 EHZ sing 294 n n C23 H46 EHZ sing 295 n n C24 H47 EHZ sing 296 n n C24 H48 EHZ sing 297 n n C25 H49 EHZ sing 298 n n C25 H50 EHZ sing 299 n n C25 H51 EHZ sing 300 n n # _atom_sites.entry_id 8XNR _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 X 24 3PE A 1 401 401 3PE 3PE . Y 25 SF4 B 1 301 236 SF4 SF4 . Z 26 PC1 B 1 302 406 PC1 PC1 . AA 27 UQ1 D 1 501 501 UQ1 UQ1 . BA 28 FES E 1 301 332 FES FES . CA 29 FMN F 1 501 521 FMN FMN . DA 25 SF4 F 1 502 522 SF4 SF4 . EA 25 SF4 G 1 801 824 SF4 SF4 . FA 25 SF4 G 1 802 825 SF4 SF4 . GA 28 FES G 1 803 826 FES FES . HA 30 UQ9 H 1 401 400 UQ9 UQ9 . IA 24 3PE H 1 402 403 3PE 3PE . JA 26 PC1 I 1 301 404 PC1 PC1 . KA 25 SF4 I 1 302 235 SF4 SF4 . LA 25 SF4 I 1 303 236 SF4 SF4 . MA 31 NDP P 1 401 536 NDP NDP . NA 32 ZN R 1 201 221 ZN ZN . OA 33 EHZ W 1 201 201 EHZ EHZ . PA 24 3PE b 1 201 201 3PE 3PE . # 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 O O1 EHZ . . . OA 33 242.743 209.187 222.061 1 60.02 0 O1 EHZ 201 W 1 HETATM 2 C C2 EHZ . . . OA 33 239.235 204.397 219.842 1 60.02 0 C2 EHZ 201 W 1 HETATM 3 C C3 EHZ . . . OA 33 239.805 205.805 219.765 1 60.02 0 C3 EHZ 201 W 1 HETATM 4 C C4 EHZ . . . OA 33 241.052 205.88 220.634 1 60.02 0 C4 EHZ 201 W 1 HETATM 5 O O2 EHZ . . . OA 33 241.316 209.215 225.557 1 60.02 0 O2 EHZ 201 W 1 HETATM 6 C C5 EHZ . . . OA 33 241.13 207.261 221.274 1 60.02 0 C5 EHZ 201 W 1 HETATM 7 C C6 EHZ . . . OA 33 241.698 207.148 222.684 1 60.02 0 C6 EHZ 201 W 1 HETATM 8 C C7 EHZ . . . OA 33 242.125 208.538 223.132 1 60.02 0 C7 EHZ 201 W 1 HETATM 9 C C8 EHZ . . . OA 33 243.107 208.434 224.289 1 60.02 0 C8 EHZ 201 W 1 HETATM 10 C C10 EHZ . . . OA 33 242.546 210.129 228.264 1 60.02 0 C10 EHZ 201 W 1 HETATM 11 C C11 EHZ . . . OA 33 243.184 211.168 229.183 1 60.02 0 C11 EHZ 201 W 1 HETATM 12 C C12 EHZ . . . OA 33 242.338 212.867 230.801 1 60.02 0 C12 EHZ 201 W 1 HETATM 13 C C13 EHZ . . . OA 33 241.307 213.879 231.272 1 60.02 0 C13 EHZ 201 W 1 HETATM 14 C C14 EHZ . . . OA 33 241.373 213.919 232.794 1 60.02 0 C14 EHZ 201 W 1 HETATM 15 C C15 EHZ . . . OA 33 240.342 215.129 234.735 1 60.02 0 C15 EHZ 201 W 1 HETATM 16 C C16 EHZ . . . OA 33 239.338 216.143 235.269 1 60.02 0 C16 EHZ 201 W 1 HETATM 17 C C17 EHZ . . . OA 33 238.468 215.586 236.395 1 60.02 0 C17 EHZ 201 W 1 HETATM 18 C C18 EHZ . . . OA 33 239.204 215.688 237.725 1 60.02 0 C18 EHZ 201 W 1 HETATM 19 C C19 EHZ . . . OA 33 237.197 216.42 236.487 1 60.02 0 C19 EHZ 201 W 1 HETATM 20 C C20 EHZ . . . OA 33 238.077 214.13 236.141 1 60.02 0 C20 EHZ 201 W 1 HETATM 21 C C9 EHZ . . . OA 33 242.491 209.161 225.474 1 60.02 0 C9 EHZ 201 W 1 HETATM 22 N N1 EHZ . . . OA 33 242.165 212.125 229.571 1 60.02 0 N1 EHZ 201 W 1 HETATM 23 N N2 EHZ . . . OA 33 240.425 214.884 233.309 1 60.02 0 N2 EHZ 201 W 1 HETATM 24 O O3 EHZ . . . OA 33 243.295 212.666 231.461 1 60.02 0 O3 EHZ 201 W 1 HETATM 25 O O4 EHZ . . . OA 33 241.062 214.557 235.474 1 60.02 0 O4 EHZ 201 W 1 HETATM 26 O O5 EHZ . . . OA 33 240.039 217.263 235.717 1 60.02 0 O5 EHZ 201 W 1 HETATM 27 O O6 EHZ . . . OA 33 236.962 213.815 236.924 1 60.02 0 O6 EHZ 201 W 1 HETATM 28 O O7 EHZ . . . OA 33 236.231 212.421 234.761 1 60.02 0 O7 EHZ 201 W 1 HETATM 29 O O9 EHZ . . . OA 33 234.475 213.385 236.38 1 60.02 -1 O9 EHZ 201 W 1 HETATM 30 P P1 EHZ . . . OA 33 235.813 212.813 236.3 1 60.02 0 P1 EHZ 201 W 1 HETATM 31 S S1 EHZ . . . OA 33 243.523 209.944 226.746 1 60.02 0 S1 EHZ 201 W 1 HETATM 32 O OP3 EHZ . . . OA 33 235.618 211.636 237.137 1 60.02 0 OP3 EHZ 201 W 1 # _model_server_stats.io_time_ms 117 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 58 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #