data_8XNY # _model_server_result.job_id LA7rfHm4Lb4KqDihOZ6kgA _model_server_result.datetime_utc '2024-12-22 09:09:10' _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 8xny # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"MA","auth_seq_id":201}' # _entry.id 8XNY # _exptl.entry_id 8XNY _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 584.703 _entity.id 31 _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 _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 31 _struct_asym.id MA _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 Q SG CYS 36 X CYS 36 1_555 Q SG CYS 66 X CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 Q SG CYS 46 X CYS 46 1_555 Q SG CYS 56 X CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 Q SG CYS 78 X CYS 78 1_555 Q SG CYS 110 X CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf4 Q SG CYS 88 X CYS 88 1_555 Q SG CYS 100 X CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc1 B SG CYS 164 B CYS 164 1_555 Z FE3 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc2 B O CYS 194 B CYS 194 1_555 Z FE2 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.713 ? metalc ? metalc3 E SG CYS 139 E CYS 139 1_555 CA FE1 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc4 E SG CYS 175 E CYS 175 1_555 CA FE2 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc5 E SG CYS 179 E CYS 179 1_555 CA FE2 FES . E FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc6 F SG CYS 385 F CYS 385 1_555 EA FE2 SF4 . F SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc7 G O PHE 63 G PHE 63 1_555 HA FE1 FES . G FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc8 G SG CYS 64 G CYS 64 1_555 HA FE1 FES . G FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc9 G SG CYS 78 G CYS 78 1_555 HA FE2 FES . G FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc10 G SG CYS 92 G CYS 92 1_555 HA FE2 FES . G FES 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? metalc ? metalc11 G NE2 HIS 124 G HIS 124 1_555 FA FE1 SF4 . G SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? metalc ? metalc12 G SG CYS 128 G CYS 128 1_555 FA FE3 SF4 . G SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc13 G SG CYS 137 G CYS 137 1_555 FA FE4 SF4 . G SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc14 I SG CYS 116 I CYS 116 1_555 JA FE4 SF4 . I SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? metalc ? metalc15 I SG CYS 158 I CYS 158 1_555 IA FE4 SF4 . I SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc16 I SG CYS 162 I CYS 162 1_555 JA FE2 SF4 . I SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc17 L SG CYS 79 R CYS 79 1_555 LA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc18 L NE2 HIS 88 R HIS 88 1_555 LA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? metalc ? metalc19 L SG CYS 104 R CYS 104 1_555 LA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc20 L SG CYS 107 R CYS 107 1_555 LA 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 8XNY _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 1 201 201 3PE 3PE . Y 24 3PE A 1 202 401 3PE 3PE . Z 25 SF4 B 1 301 236 SF4 SF4 . AA 26 PC1 B 1 302 406 PC1 PC1 . BA 26 PC1 B 1 303 436 PC1 PC1 . CA 27 FES E 1 301 332 FES FES . DA 28 FMN F 1 501 521 FMN FMN . EA 25 SF4 F 1 502 522 SF4 SF4 . FA 25 SF4 G 1 801 824 SF4 SF4 . GA 25 SF4 G 1 802 825 SF4 SF4 . HA 27 FES G 1 803 826 FES FES . IA 25 SF4 I 1 301 235 SF4 SF4 . JA 25 SF4 I 1 302 236 SF4 SF4 . KA 29 NDP P 1 401 536 NDP NDP . LA 30 ZN R 1 201 221 ZN ZN . MA 31 EHZ W 1 201 201 EHZ EHZ . # 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 . . . MA 31 247.536 202.851 224.748 1 42.29 0 O1 EHZ 201 W 1 HETATM 2 C C1 EHZ . . . MA 31 243.701 199.94 220.16 1 42.29 0 C1 EHZ 201 W 1 HETATM 3 C C2 EHZ . . . MA 31 245.146 200.164 220.601 1 42.29 0 C2 EHZ 201 W 1 HETATM 4 C C3 EHZ . . . MA 31 245.307 199.701 222.045 1 42.29 0 C3 EHZ 201 W 1 HETATM 5 C C4 EHZ . . . MA 31 246.014 200.781 222.858 1 42.29 0 C4 EHZ 201 W 1 HETATM 6 O O2 EHZ . . . MA 31 246.399 203.923 226.598 1 42.29 0 O2 EHZ 201 W 1 HETATM 7 C C5 EHZ . . . MA 31 245.546 202.16 222.407 1 42.29 0 C5 EHZ 201 W 1 HETATM 8 C C6 EHZ . . . MA 31 245.44 203.07 223.627 1 42.29 0 C6 EHZ 201 W 1 HETATM 9 C C7 EHZ . . . MA 31 246.804 203.69 223.903 1 42.29 0 C7 EHZ 201 W 1 HETATM 10 C C8 EHZ . . . MA 31 246.634 205.062 224.545 1 42.29 0 C8 EHZ 201 W 1 HETATM 11 C C10 EHZ . . . MA 31 246.126 206.283 228.661 1 42.29 0 C10 EHZ 201 W 1 HETATM 12 C C11 EHZ . . . MA 31 247.177 205.984 229.722 1 42.29 0 C11 EHZ 201 W 1 HETATM 13 C C12 EHZ . . . MA 31 246.341 207.759 231.316 1 42.29 0 C12 EHZ 201 W 1 HETATM 14 C C13 EHZ . . . MA 31 245.861 208.13 232.713 1 42.29 0 C13 EHZ 201 W 1 HETATM 15 C C14 EHZ . . . MA 31 244.822 207.115 233.179 1 42.29 0 C14 EHZ 201 W 1 HETATM 16 C C15 EHZ . . . MA 31 244.687 208.151 235.477 1 42.29 0 C15 EHZ 201 W 1 HETATM 17 C C16 EHZ . . . MA 31 244.728 207.994 236.99 1 42.29 0 C16 EHZ 201 W 1 HETATM 18 C C17 EHZ . . . MA 31 243.311 207.996 237.558 1 42.29 0 C17 EHZ 201 W 1 HETATM 19 C C18 EHZ . . . MA 31 243.129 206.805 238.494 1 42.29 0 C18 EHZ 201 W 1 HETATM 20 C C19 EHZ . . . MA 31 243.099 209.292 238.335 1 42.29 0 C19 EHZ 201 W 1 HETATM 21 C C20 EHZ . . . MA 31 242.282 207.931 236.435 1 42.29 0 C20 EHZ 201 W 1 HETATM 22 C C21 EHZ . . . MA 31 243.687 199.384 218.74 1 42.29 0 C21 EHZ 201 W 1 HETATM 23 C C22 EHZ . . . MA 31 244.659 198.21 218.654 1 42.29 0 C22 EHZ 201 W 1 HETATM 24 C C9 EHZ . . . MA 31 246.633 204.954 226.068 1 42.29 0 C9 EHZ 201 W 1 HETATM 25 N N1 EHZ . . . MA 31 246.707 206.387 231.031 1 42.29 0 N1 EHZ 201 W 1 HETATM 26 N N2 EHZ . . . MA 31 244.864 206.992 234.623 1 42.29 0 N2 EHZ 201 W 1 HETATM 27 O O3 EHZ . . . MA 31 246.411 208.589 230.48 1 42.29 0 O3 EHZ 201 W 1 HETATM 28 O O4 EHZ . . . MA 31 244.507 209.223 235.014 1 42.29 0 O4 EHZ 201 W 1 HETATM 29 O O5 EHZ . . . MA 31 245.386 206.804 237.324 1 42.29 0 O5 EHZ 201 W 1 HETATM 30 O O6 EHZ . . . MA 31 241.679 206.669 236.403 1 42.29 0 O6 EHZ 201 W 1 HETATM 31 O O7 EHZ . . . MA 31 239.654 205.058 235.639 1 42.29 0 O7 EHZ 201 W 1 HETATM 32 O O9 EHZ . . . MA 31 239.27 207.075 237.185 1 42.29 -1 O9 EHZ 201 W 1 HETATM 33 P P1 EHZ . . . MA 31 240.069 206.593 236.065 1 42.29 0 P1 EHZ 201 W 1 HETATM 34 S S1 EHZ . . . MA 31 246.986 206.419 227.074 1 42.29 0 S1 EHZ 201 W 1 HETATM 35 O OP3 EHZ . . . MA 31 239.701 207.547 235.026 1 42.29 0 OP3 EHZ 201 W 1 # _model_server_stats.io_time_ms 48 _model_server_stats.parse_time_ms 68 _model_server_stats.create_model_time_ms 230 _model_server_stats.query_time_ms 1549 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 35 #