data_8XNV # _model_server_result.job_id jLQHSdf9kEoPW-GShpZtdQ _model_server_result.datetime_utc '2024-11-30 17:51:54' _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 8xnv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"PA","auth_seq_id":201}' # _entry.id 8XNV # _exptl.entry_id 8XNV _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,QA _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 PA _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 Q SG CYS 46 X CYS 46 1_555 Q SG CYS 56 X CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf3 Q SG CYS 78 X CYS 78 1_555 Q SG CYS 110 X CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 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 Y FE3 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc2 B O CYS 194 B CYS 194 1_555 Y FE2 SF4 . B SF4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.745 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc6 F SG CYS 385 F CYS 385 1_555 EA FE2 SF4 . F SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc14 I SG CYS 116 I CYS 116 1_555 MA FE4 SF4 . I SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc15 I SG CYS 119 I CYS 119 1_555 MA FE1 SF4 . I SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc16 I SG CYS 158 I CYS 158 1_555 LA FE4 SF4 . I SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc17 I SG CYS 162 I CYS 162 1_555 MA FE2 SF4 . I SF4 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc18 L SG CYS 79 R CYS 79 1_555 OA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc19 L NE2 HIS 88 R HIS 88 1_555 OA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? metalc ? metalc20 L SG CYS 104 R CYS 104 1_555 OA ZN ZN . R ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc21 L SG CYS 107 R CYS 107 1_555 OA 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 470 n n O9 P1 EHZ doub 471 n n P1 O6 EHZ sing 472 n n O6 C20 EHZ sing 473 n n C20 C17 EHZ sing 474 n n O5 C16 EHZ sing 475 n n C19 C17 EHZ sing 476 n n C17 C16 EHZ sing 477 n n C17 C18 EHZ sing 478 n n C16 C15 EHZ sing 479 n n C15 O4 EHZ doub 480 n n C15 N2 EHZ sing 481 n n N2 C14 EHZ sing 482 n n C13 C14 EHZ sing 483 n n C13 C12 EHZ sing 484 n n N1 C12 EHZ sing 485 n n N1 C11 EHZ sing 486 n n C12 O3 EHZ doub 487 n n C11 C10 EHZ sing 488 n n O2 C9 EHZ doub 489 n n C10 S1 EHZ sing 490 n n C7 C6 EHZ sing 491 n n C7 C8 EHZ sing 492 n n C7 O1 EHZ sing 493 n n C9 S1 EHZ sing 494 n n C9 C8 EHZ sing 495 n n C6 C5 EHZ sing 496 n n C22 C21 EHZ sing 497 n n C1 C21 EHZ sing 498 n n C1 C2 EHZ sing 499 n n C3 C2 EHZ sing 500 n n C3 C4 EHZ sing 501 n n C5 C4 EHZ sing 502 n n O1 H1 EHZ sing 503 n n C1 H2 EHZ sing 504 n n C1 H3 EHZ sing 505 n n C2 H4 EHZ sing 506 n n C2 H5 EHZ sing 507 n n C3 H6 EHZ sing 508 n n C3 H7 EHZ sing 509 n n C4 H8 EHZ sing 510 n n C4 H9 EHZ sing 511 n n C5 H10 EHZ sing 512 n n C5 H11 EHZ sing 513 n n C6 H12 EHZ sing 514 n n C6 H13 EHZ sing 515 n n C7 H14 EHZ sing 516 n n C8 H15 EHZ sing 517 n n C8 H16 EHZ sing 518 n n C10 H17 EHZ sing 519 n n C10 H18 EHZ sing 520 n n C11 H19 EHZ sing 521 n n C11 H20 EHZ sing 522 n n C13 H21 EHZ sing 523 n n C13 H22 EHZ sing 524 n n C14 H23 EHZ sing 525 n n C14 H24 EHZ sing 526 n n C16 H25 EHZ sing 527 n n C18 H26 EHZ sing 528 n n C18 H27 EHZ sing 529 n n C18 H28 EHZ sing 530 n n C19 H29 EHZ sing 531 n n C19 H30 EHZ sing 532 n n C19 H31 EHZ sing 533 n n C20 H32 EHZ sing 534 n n C20 H33 EHZ sing 535 n n C21 H34 EHZ sing 536 n n C21 H35 EHZ sing 537 n n C22 H36 EHZ sing 538 n n C22 H37 EHZ sing 539 n n N1 H39 EHZ sing 540 n n N2 H40 EHZ sing 541 n n O5 H41 EHZ sing 542 n n O7 H42 EHZ sing 543 n n P1 OP3 EHZ sing 544 n n C22 C23 EHZ sing 545 n n C23 C24 EHZ sing 546 n n C24 C25 EHZ sing 547 n n OP3 H44 EHZ sing 548 n n C23 H45 EHZ sing 549 n n C23 H46 EHZ sing 550 n n C24 H47 EHZ sing 551 n n C24 H48 EHZ sing 552 n n C25 H49 EHZ sing 553 n n C25 H50 EHZ sing 554 n n C25 H51 EHZ sing 555 n n # _atom_sites.entry_id 8XNV _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 25 SF4 B 1 301 236 SF4 SF4 . Z 26 PC1 B 1 302 406 PC1 PC1 . AA 26 PC1 B 1 303 436 PC1 PC1 . BA 27 UQ1 D 1 501 502 UQ1 UQ1 . CA 28 FES E 1 301 332 FES FES . DA 29 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 28 FES G 1 803 826 FES FES . IA 30 UQ9 H 1 400 400 UQ9 UQ9 . JA 24 3PE H 1 401 401 3PE 3PE . KA 24 3PE I 1 301 403 3PE 3PE . LA 25 SF4 I 1 302 235 SF4 SF4 . MA 25 SF4 I 1 303 236 SF4 SF4 . NA 31 NDP P 1 401 536 NDP NDP . OA 32 ZN R 1 201 221 ZN ZN . PA 33 EHZ W 1 201 201 EHZ EHZ . QA 34 CDL a 1 101 405 CDL CDL . # 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 . . . PA 33 243.447 207.989 225.543 1 42.29 0 O1 EHZ 201 W 1 HETATM 2 C C1 EHZ . . . PA 33 239.663 205.019 220.951 1 42.29 0 C1 EHZ 201 W 1 HETATM 3 C C2 EHZ . . . PA 33 241.095 205.185 221.451 1 42.29 0 C2 EHZ 201 W 1 HETATM 4 C C3 EHZ . . . PA 33 241.158 204.808 222.928 1 42.29 0 C3 EHZ 201 W 1 HETATM 5 C C4 EHZ . . . PA 33 241.891 205.894 223.708 1 42.29 0 C4 EHZ 201 W 1 HETATM 6 O O2 EHZ . . . PA 33 242.292 209.245 227.262 1 42.29 0 O2 EHZ 201 W 1 HETATM 7 C C5 EHZ . . . PA 33 241.532 207.267 223.15 1 42.29 0 C5 EHZ 201 W 1 HETATM 8 C C6 EHZ . . . PA 33 241.425 208.259 224.303 1 42.29 0 C6 EHZ 201 W 1 HETATM 9 C C7 EHZ . . . PA 33 242.81 208.813 224.611 1 42.29 0 C7 EHZ 201 W 1 HETATM 10 C C8 EHZ . . . PA 33 242.696 210.232 225.157 1 42.29 0 C8 EHZ 201 W 1 HETATM 11 C C10 EHZ . . . PA 33 242.068 211.745 229.157 1 42.29 0 C10 EHZ 201 W 1 HETATM 12 C C11 EHZ . . . PA 33 243.045 211.455 230.288 1 42.29 0 C11 EHZ 201 W 1 HETATM 13 C C12 EHZ . . . PA 33 242.246 213.376 231.723 1 42.29 0 C12 EHZ 201 W 1 HETATM 14 C C13 EHZ . . . PA 33 241.724 213.864 233.068 1 42.29 0 C13 EHZ 201 W 1 HETATM 15 C C14 EHZ . . . PA 33 240.602 212.945 233.541 1 42.29 0 C14 EHZ 201 W 1 HETATM 16 C C15 EHZ . . . PA 33 240.422 214.134 235.76 1 42.29 0 C15 EHZ 201 W 1 HETATM 17 C C16 EHZ . . . PA 33 240.381 214.073 237.281 1 42.29 0 C16 EHZ 201 W 1 HETATM 18 C C17 EHZ . . . PA 33 238.94 214.197 237.774 1 42.29 0 C17 EHZ 201 W 1 HETATM 19 C C18 EHZ . . . PA 33 238.64 213.082 238.771 1 42.29 0 C18 EHZ 201 W 1 HETATM 20 C C19 EHZ . . . PA 33 238.773 215.55 238.456 1 42.29 0 C19 EHZ 201 W 1 HETATM 21 C C20 EHZ . . . PA 33 237.964 214.119 236.604 1 42.29 0 C20 EHZ 201 W 1 HETATM 22 C C21 EHZ . . . PA 33 239.682 204.373 219.569 1 42.29 0 C21 EHZ 201 W 1 HETATM 23 C C22 EHZ . . . PA 33 240.582 203.141 219.607 1 42.29 0 C22 EHZ 201 W 1 HETATM 24 C C9 EHZ . . . PA 33 242.615 210.223 226.681 1 42.29 0 C9 EHZ 201 W 1 HETATM 25 N N1 EHZ . . . PA 33 242.539 211.968 231.544 1 42.29 0 N1 EHZ 201 W 1 HETATM 26 N N2 EHZ . . . PA 33 240.567 212.913 234.991 1 42.29 0 N2 EHZ 201 W 1 HETATM 27 O O3 EHZ . . . PA 33 242.408 214.144 230.842 1 42.29 0 O3 EHZ 201 W 1 HETATM 28 O O4 EHZ . . . PA 33 240.332 215.183 235.224 1 42.29 0 O4 EHZ 201 W 1 HETATM 29 O O5 EHZ . . . PA 33 240.946 212.871 237.722 1 42.29 0 O5 EHZ 201 W 1 HETATM 30 O O6 EHZ . . . PA 33 237.286 212.896 236.619 1 42.29 0 O6 EHZ 201 W 1 HETATM 31 O O7 EHZ . . . PA 33 235.203 211.362 235.852 1 42.29 0 O7 EHZ 201 W 1 HETATM 32 O O9 EHZ . . . PA 33 234.872 213.494 237.249 1 42.29 -1 O9 EHZ 201 W 1 HETATM 33 P P1 EHZ . . . PA 33 235.693 212.894 236.203 1 42.29 0 P1 EHZ 201 W 1 HETATM 34 S S1 EHZ . . . PA 33 243.009 211.727 227.612 1 42.29 0 S1 EHZ 201 W 1 HETATM 35 O OP3 EHZ . . . PA 33 235.435 213.799 235.09 1 42.29 0 OP3 EHZ 201 W 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 124 _model_server_stats.query_time_ms 439 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 35 #