6UXE
Structure of the human mitochondrial desulfurase complex Nfs1-ISCU2(M140I)-ISD11 with E.coli ACP1 at 1.57 A resolution showing flexibility of N terminal end of ISCU2
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0030170 | molecular_function | pyridoxal phosphate binding |
A | 0031071 | molecular_function | cysteine desulfurase activity |
A | 0044571 | biological_process | [2Fe-2S] cluster assembly |
B | 0005515 | molecular_function | protein binding |
B | 0005634 | cellular_component | nucleus |
B | 0005739 | cellular_component | mitochondrion |
B | 0005759 | cellular_component | mitochondrial matrix |
B | 0016226 | biological_process | iron-sulfur cluster assembly |
B | 0016604 | cellular_component | nuclear body |
B | 0042803 | molecular_function | protein homodimerization activity |
B | 0044571 | biological_process | [2Fe-2S] cluster assembly |
B | 0044572 | biological_process | [4Fe-4S] cluster assembly |
B | 0099128 | cellular_component | mitochondrial [2Fe-2S] assembly complex |
B | 1990221 | cellular_component | L-cysteine desulfurase complex |
B | 1990229 | cellular_component | iron-sulfur cluster assembly complex |
C | 0000035 | molecular_function | acyl binding |
C | 0000036 | molecular_function | acyl carrier activity |
C | 0005515 | molecular_function | protein binding |
C | 0005737 | cellular_component | cytoplasm |
C | 0005829 | cellular_component | cytosol |
C | 0006633 | biological_process | fatty acid biosynthetic process |
C | 0008289 | molecular_function | lipid binding |
C | 0008610 | biological_process | lipid biosynthetic process |
C | 0009245 | biological_process | lipid A biosynthetic process |
C | 0009410 | biological_process | response to xenobiotic stimulus |
C | 0031177 | molecular_function | phosphopantetheine binding |
D | 0005506 | molecular_function | iron ion binding |
D | 0016226 | biological_process | iron-sulfur cluster assembly |
D | 0051536 | molecular_function | iron-sulfur cluster binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 16 |
Details | binding site for residue PLP A 501 |
Chain | Residue |
A | GLY126 |
A | SER255 |
A | HIS257 |
A | LYS258 |
A | THR295 |
A | CYS381 |
A | HOH636 |
A | HOH776 |
A | ALA127 |
A | THR128 |
A | HIS156 |
A | MET203 |
A | ASN207 |
A | ASP232 |
A | ALA234 |
A | GLN235 |
site_id | AC2 |
Number of Residues | 10 |
Details | binding site for residue GOL A 502 |
Chain | Residue |
A | PRO58 |
A | THR92 |
A | HIS93 |
A | ALA94 |
A | LEU367 |
A | MET368 |
A | LEU370 |
A | LYS371 |
A | EDO509 |
D | TYR35 |
site_id | AC3 |
Number of Residues | 5 |
Details | binding site for residue GOL A 503 |
Chain | Residue |
A | ARG321 |
A | THR415 |
A | GLU416 |
A | GLU417 |
B | ARG34 |
site_id | AC4 |
Number of Residues | 6 |
Details | binding site for residue GOL A 504 |
Chain | Residue |
A | LYS431 |
A | ARG434 |
A | GLU435 |
A | TRP440 |
A | HOH678 |
A | HOH801 |
site_id | AC5 |
Number of Residues | 7 |
Details | binding site for residue GOL A 505 |
Chain | Residue |
A | GLU190 |
A | ARG220 |
A | ILE221 |
A | SER224 |
A | ARG225 |
A | HOH619 |
A | HOH633 |
site_id | AC6 |
Number of Residues | 7 |
Details | binding site for residue EDO A 506 |
Chain | Residue |
A | GLN179 |
A | ASP185 |
A | LYS371 |
A | ARG432 |
A | EDO507 |
A | EDO530 |
D | GLU44 |
site_id | AC7 |
Number of Residues | 9 |
Details | binding site for residue EDO A 507 |
Chain | Residue |
A | MET368 |
A | ALA369 |
A | LYS371 |
A | HIS429 |
A | EDO506 |
A | EDO530 |
D | VAL40 |
D | TYR43 |
D | GLU44 |
site_id | AC8 |
Number of Residues | 4 |
Details | binding site for residue EDO A 508 |
Chain | Residue |
A | MET334 |
A | LYS335 |
A | LEU337 |
A | PRO338 |
site_id | AC9 |
Number of Residues | 5 |
Details | binding site for residue EDO A 509 |
Chain | Residue |
A | PRO58 |
A | LYS371 |
A | GOL502 |
A | HOH624 |
A | HOH698 |
site_id | AD1 |
Number of Residues | 4 |
Details | binding site for residue EDO A 510 |
Chain | Residue |
A | LYS157 |
A | TYR390 |
A | PEG527 |
A | HOH653 |
site_id | AD2 |
Number of Residues | 5 |
Details | binding site for residue EDO A 511 |
Chain | Residue |
A | ARG105 |
A | GLN108 |
A | EDO517 |
A | HOH617 |
A | HOH781 |
site_id | AD3 |
Number of Residues | 5 |
Details | binding site for residue EDO A 512 |
Chain | Residue |
A | GLU100 |
A | ALA101 |
A | HOH617 |
A | HOH671 |
A | HOH800 |
site_id | AD4 |
Number of Residues | 6 |
Details | binding site for residue EDO A 513 |
Chain | Residue |
A | SER223 |
A | LYS248 |
A | ASP250 |
A | ARG271 |
A | GOL551 |
A | HOH609 |
site_id | AD5 |
Number of Residues | 8 |
Details | binding site for residue EDO A 514 |
Chain | Residue |
A | SER125 |
A | ARG292 |
A | THR295 |
A | PRO297 |
A | HOH636 |
A | HOH675 |
A | HOH675 |
A | HOH682 |
site_id | AD6 |
Number of Residues | 4 |
Details | binding site for residue EDO A 515 |
Chain | Residue |
A | HOH710 |
B | PEG104 |
A | GLU316 |
A | LYS320 |
site_id | AD7 |
Number of Residues | 6 |
Details | binding site for residue EDO A 516 |
Chain | Residue |
A | GLN179 |
A | SER181 |
A | ASP345 |
A | HOH604 |
A | HOH610 |
D | ASN45 |
site_id | AD8 |
Number of Residues | 6 |
Details | binding site for residue EDO A 517 |
Chain | Residue |
A | GLU104 |
A | GLN108 |
A | PRO118 |
A | EDO511 |
A | HOH651 |
A | HOH762 |
site_id | AD9 |
Number of Residues | 8 |
Details | binding site for residue PEG A 518 |
Chain | Residue |
A | ASP75 |
A | PRO79 |
A | HOH841 |
B | ARG68 |
B | LEU75 |
B | TYR76 |
B | SER77 |
B | HOH218 |
site_id | AE1 |
Number of Residues | 10 |
Details | binding site for residue PG4 A 519 |
Chain | Residue |
A | SER112 |
A | GLY115 |
A | ALA116 |
A | GLN312 |
A | GLN313 |
A | EDO525 |
A | PEG550 |
A | HOH645 |
A | HOH745 |
A | HOH753 |
site_id | AE2 |
Number of Residues | 4 |
Details | binding site for residue PG4 A 520 |
Chain | Residue |
A | ARG328 |
A | ASN332 |
A | HOH667 |
A | HOH670 |
site_id | AE3 |
Number of Residues | 1 |
Details | binding site for residue PEG A 521 |
Chain | Residue |
A | HIS319 |
site_id | AE4 |
Number of Residues | 6 |
Details | binding site for residue EDO A 522 |
Chain | Residue |
A | ALA359 |
A | TYR360 |
A | ASP400 |
A | SER404 |
A | LEU439 |
A | P15526 |
site_id | AE5 |
Number of Residues | 5 |
Details | binding site for residue EDO A 523 |
Chain | Residue |
A | ARG220 |
A | SER224 |
A | LYS248 |
D | ARG89 |
D | EDO202 |
site_id | AE6 |
Number of Residues | 2 |
Details | binding site for residue EDO A 524 |
Chain | Residue |
A | ARG119 |
A | ARG272 |
site_id | AE7 |
Number of Residues | 3 |
Details | binding site for residue EDO A 525 |
Chain | Residue |
A | GLN312 |
A | GLN313 |
A | PG4519 |
site_id | AE8 |
Number of Residues | 13 |
Details | binding site for residue P15 A 526 |
Chain | Residue |
A | LEU337 |
A | PRO338 |
A | ASP339 |
A | VAL340 |
A | VAL341 |
A | ALA359 |
A | ASP400 |
A | LEU401 |
A | LEU449 |
A | EDO522 |
A | HOH612 |
A | HOH615 |
A | HOH729 |
site_id | AE9 |
Number of Residues | 4 |
Details | binding site for residue PEG A 527 |
Chain | Residue |
A | GLN153 |
A | TYR175 |
A | EDO510 |
A | PEG531 |
site_id | AF1 |
Number of Residues | 4 |
Details | binding site for residue EDO A 528 |
Chain | Residue |
A | GLN108 |
A | ASP117 |
A | PRO118 |
A | HOH634 |
site_id | AF2 |
Number of Residues | 3 |
Details | binding site for residue EDO A 529 |
Chain | Residue |
A | GLN313 |
A | EDO545 |
B | ARG35 |
site_id | AF3 |
Number of Residues | 7 |
Details | binding site for residue EDO A 530 |
Chain | Residue |
A | LYS371 |
A | LYS425 |
A | GLN428 |
A | HIS429 |
A | EDO506 |
A | EDO507 |
A | HOH601 |
site_id | AF4 |
Number of Residues | 5 |
Details | binding site for residue PEG A 531 |
Chain | Residue |
A | GLU167 |
A | VAL173 |
A | THR174 |
A | TYR175 |
A | PEG527 |
site_id | AF5 |
Number of Residues | 2 |
Details | binding site for residue PEG A 532 |
Chain | Residue |
A | GLN331 |
A | PGE534 |
site_id | AF6 |
Number of Residues | 7 |
Details | binding site for residue DTT A 533 |
Chain | Residue |
A | GLU120 |
A | VAL244 |
A | ASN245 |
A | TYR269 |
A | ARG271 |
A | ARG273 |
A | PEG550 |
site_id | AF7 |
Number of Residues | 11 |
Details | binding site for residue PGE A 534 |
Chain | Residue |
A | HIS319 |
A | SER323 |
A | SER326 |
A | ILE330 |
A | PRO346 |
A | HIS349 |
A | PRO351 |
A | PEG532 |
A | EDO552 |
A | HOH602 |
A | HOH607 |
site_id | AF8 |
Number of Residues | 4 |
Details | binding site for residue EDO A 535 |
Chain | Residue |
A | GLU416 |
A | GLU417 |
A | ASP420 |
A | HOH727 |
site_id | AF9 |
Number of Residues | 6 |
Details | binding site for residue EDO A 536 |
Chain | Residue |
A | GLU217 |
A | ARG220 |
A | HOH659 |
A | HOH819 |
D | ARG47 |
D | ASN48 |
site_id | AG1 |
Number of Residues | 3 |
Details | binding site for residue EDO A 537 |
Chain | Residue |
A | ASP420 |
A | TYR421 |
A | HOH727 |
site_id | AG2 |
Number of Residues | 6 |
Details | binding site for residue EDO A 538 |
Chain | Residue |
A | LYS212 |
A | GLN213 |
A | HOH647 |
A | HOH649 |
A | HOH659 |
A | HOH740 |
site_id | AG3 |
Number of Residues | 4 |
Details | binding site for residue EDO A 539 |
Chain | Residue |
A | LYS180 |
A | ARG393 |
A | ALA394 |
A | HOH662 |
site_id | AG4 |
Number of Residues | 2 |
Details | binding site for residue EDO A 540 |
Chain | Residue |
A | PHE141 |
A | EDO542 |
site_id | AG5 |
Number of Residues | 4 |
Details | binding site for residue EDO A 541 |
Chain | Residue |
A | GLN428 |
A | ARG432 |
A | HOH608 |
A | HOH771 |
site_id | AG6 |
Number of Residues | 5 |
Details | binding site for residue EDO A 542 |
Chain | Residue |
A | PHE141 |
A | TYR142 |
A | ARG143 |
A | SER144 |
A | EDO540 |
site_id | AG7 |
Number of Residues | 11 |
Details | binding site for residue PGE A 543 |
Chain | Residue |
A | ARG105 |
A | GLN109 |
A | ALA306 |
A | GLU309 |
A | VAL310 |
A | GLN313 |
A | HOH646 |
A | HOH680 |
B | ARG61 |
B | HOH221 |
B | HOH260 |
site_id | AG8 |
Number of Residues | 2 |
Details | binding site for residue PGE A 544 |
Chain | Residue |
A | ARG105 |
A | HOH614 |
site_id | AG9 |
Number of Residues | 4 |
Details | binding site for residue EDO A 545 |
Chain | Residue |
A | GLU314 |
A | EDO529 |
A | HOH742 |
B | ARG35 |
site_id | AH1 |
Number of Residues | 6 |
Details | binding site for residue EDO A 546 |
Chain | Residue |
A | ILE270 |
A | ARG271 |
A | ARG272 |
A | ARG275 |
A | VAL276 |
A | HOH605 |
site_id | AH2 |
Number of Residues | 4 |
Details | binding site for residue EDO A 547 |
Chain | Residue |
A | GLY286 |
A | GLN287 |
A | EDO553 |
A | HOH754 |
site_id | AH3 |
Number of Residues | 2 |
Details | binding site for residue PEG A 548 |
Chain | Residue |
A | GLU441 |
A | MET442 |
site_id | AH4 |
Number of Residues | 5 |
Details | binding site for residue PEG A 549 |
Chain | Residue |
A | ASP161 |
A | SER283 |
A | GLY284 |
A | EDO554 |
A | HOH722 |
site_id | AH5 |
Number of Residues | 8 |
Details | binding site for residue PEG A 550 |
Chain | Residue |
A | GLY115 |
A | ALA116 |
A | ASP117 |
A | ASP243 |
A | PG4519 |
A | DTT533 |
A | HOH634 |
A | HOH677 |
site_id | AH6 |
Number of Residues | 7 |
Details | binding site for residue GOL A 551 |
Chain | Residue |
A | SER223 |
A | LYS226 |
A | VAL227 |
A | ASP250 |
A | EDO513 |
A | HOH621 |
A | HOH637 |
site_id | AH7 |
Number of Residues | 8 |
Details | binding site for residue EDO A 552 |
Chain | Residue |
A | LYS212 |
A | PRO346 |
A | LYS347 |
A | HIS348 |
A | HIS349 |
A | PGE534 |
A | HOH607 |
A | HOH740 |
site_id | AH8 |
Number of Residues | 7 |
Details | binding site for residue EDO A 553 |
Chain | Residue |
A | GLY286 |
A | GLN287 |
A | GLU288 |
A | ARG289 |
A | EDO547 |
A | HOH717 |
A | HOH824 |
site_id | AH9 |
Number of Residues | 9 |
Details | binding site for residue EDO A 554 |
Chain | Residue |
A | ALA280 |
A | GLN282 |
A | GLY284 |
A | GLY290 |
A | MET291 |
A | ARG292 |
A | SER293 |
A | PEG549 |
A | HOH782 |
site_id | AI1 |
Number of Residues | 7 |
Details | binding site for residue EDO B 101 |
Chain | Residue |
A | VAL63 |
A | PRO68 |
A | TYR85 |
A | PHE413 |
A | HOH721 |
B | ASN27 |
B | HOH202 |
site_id | AI2 |
Number of Residues | 7 |
Details | binding site for residue EDO B 102 |
Chain | Residue |
A | ASP445 |
B | ALA11 |
B | LEU12 |
B | HOH208 |
B | HOH220 |
B | HOH255 |
B | HOH257 |
site_id | AI3 |
Number of Residues | 4 |
Details | binding site for residue EDO B 103 |
Chain | Residue |
B | ARG18 |
B | ARG22 |
B | HOH224 |
B | HOH226 |
site_id | AI4 |
Number of Residues | 7 |
Details | binding site for residue PEG B 104 |
Chain | Residue |
A | TYR317 |
A | EDO515 |
B | ARG35 |
B | ASP38 |
B | ALA39 |
B | GLU42 |
B | HOH245 |
site_id | AI5 |
Number of Residues | 5 |
Details | binding site for residue EDO B 105 |
Chain | Residue |
A | ASP445 |
A | GLY446 |
B | ARG67 |
B | PEG106 |
B | EDO107 |
site_id | AI6 |
Number of Residues | 5 |
Details | binding site for residue PEG B 106 |
Chain | Residue |
B | ARG67 |
B | ARG68 |
B | LEU75 |
B | EDO105 |
B | EDO107 |
site_id | AI7 |
Number of Residues | 8 |
Details | binding site for residue EDO B 107 |
Chain | Residue |
A | GLY446 |
B | GLY64 |
B | ARG67 |
B | ARG68 |
B | EDO105 |
B | PEG106 |
B | HOH201 |
B | HOH242 |
site_id | AI8 |
Number of Residues | 2 |
Details | binding site for residue EDO B 108 |
Chain | Residue |
B | GLU42 |
B | ASN43 |
site_id | AI9 |
Number of Residues | 5 |
Details | binding site for residue EDO B 109 |
Chain | Residue |
B | LYS21 |
B | ARG22 |
B | PHE23 |
B | ARG29 |
B | EDT110 |
site_id | AJ1 |
Number of Residues | 9 |
Details | binding site for residue EDT B 110 |
Chain | Residue |
A | GLU417 |
B | LYS21 |
B | TYR26 |
B | ARG29 |
B | LYS80 |
B | ILE83 |
B | GLU84 |
B | EDO109 |
B | HOH231 |
site_id | AJ2 |
Number of Residues | 4 |
Details | binding site for residue EDO B 111 |
Chain | Residue |
A | ILE193 |
A | ARG225 |
B | HOH206 |
B | HOH251 |
site_id | AJ3 |
Number of Residues | 7 |
Details | binding site for residue EDO B 112 |
Chain | Residue |
A | LYS187 |
A | GLU190 |
A | GLU435 |
A | HOH628 |
B | ALA2 |
B | ALA3 |
B | HOH235 |
site_id | AJ4 |
Number of Residues | 13 |
Details | binding site for residue 8Q1 C 301 |
Chain | Residue |
B | ARG6 |
B | VAL9 |
B | ALA39 |
B | PHE40 |
B | ASN43 |
B | LYS44 |
B | VAL46 |
B | ILE52 |
B | HOH243 |
C | ASP35 |
C | SER36 |
C | EDO303 |
C | HOH415 |
site_id | AJ5 |
Number of Residues | 6 |
Details | binding site for residue MES C 302 |
Chain | Residue |
B | ARG41 |
B | LYS44 |
C | LEU15 |
C | GLY33 |
C | ASP35 |
C | ASP38 |
site_id | AJ6 |
Number of Residues | 5 |
Details | binding site for residue EDO C 303 |
Chain | Residue |
C | VAL29 |
C | ASP35 |
C | SER36 |
C | 8Q1301 |
C | HOH401 |
site_id | AJ7 |
Number of Residues | 4 |
Details | binding site for residue EDO C 304 |
Chain | Residue |
C | GLN14 |
C | ASP38 |
C | GLU41 |
C | LEU42 |
site_id | AJ8 |
Number of Residues | 5 |
Details | binding site for residue PEG C 305 |
Chain | Residue |
B | LYS21 |
C | GLN14 |
C | GLU41 |
C | MET44 |
C | GLU48 |
site_id | AJ9 |
Number of Residues | 3 |
Details | binding site for residue EDO C 306 |
Chain | Residue |
C | TYR71 |
C | HIS75 |
D | LYS57 |
site_id | AK1 |
Number of Residues | 7 |
Details | binding site for residue EDO D 201 |
Chain | Residue |
A | GLU441 |
A | HOH628 |
A | HOH633 |
D | GLY50 |
D | SER51 |
D | LYS91 |
D | EDO202 |
site_id | AK2 |
Number of Residues | 6 |
Details | binding site for residue EDO D 202 |
Chain | Residue |
A | ARG220 |
A | EDO523 |
D | GLY50 |
D | SER51 |
D | ARG89 |
D | EDO201 |
site_id | AK3 |
Number of Residues | 7 |
Details | binding site for residue 1PE D 203 |
Chain | Residue |
D | TRP108 |
D | GLY111 |
D | LYS112 |
D | GLU116 |
D | THR119 |
D | ILE120 |
D | HOH312 |
site_id | AK4 |
Number of Residues | 2 |
Details | binding site for residue EDO D 204 |
Chain | Residue |
D | THR61 |
D | ASP152 |
site_id | AK5 |
Number of Residues | 6 |
Details | binding site for residue GOL D 205 |
Chain | Residue |
B | ARG14 |
C | ASP56 |
D | ASP53 |
D | THR55 |
D | HOH305 |
D | HOH320 |
site_id | AK6 |
Number of Residues | 2 |
Details | binding site for residue EDO D 206 |
Chain | Residue |
D | ASP80 |
D | HOH302 |
site_id | AK7 |
Number of Residues | 3 |
Details | binding site for residue EDO D 207 |
Chain | Residue |
D | GLU107 |
D | HOH321 |
D | HOH336 |
Functional Information from PROSITE/UniProt
site_id | PS00012 |
Number of Residues | 16 |
Details | PHOSPHOPANTETHEINE Phosphopantetheine attachment site. DLGADSLDTVELVMAL |
Chain | Residue | Details |
C | ASP31-LEU46 |
site_id | PS00595 |
Number of Residues | 20 |
Details | AA_TRANSFER_CLASS_5 Aminotransferases class-V pyridoxal-phosphate attachment site. IDLMsiSGHKiygpk.GvGaI |
Chain | Residue | Details |
A | ILE249-ILE268 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 1 |
Details | ACT_SITE: Cysteine persulfide intermediate => ECO:0000250|UniProtKB:Q9D7P6 |
Chain | Residue | Details |
D | CYS69 | |
B | LYS44 |
site_id | SWS_FT_FI2 |
Number of Residues | 1 |
Details | ACT_SITE: Cysteine persulfide intermediate => ECO:0000250|UniProtKB:O29689 |
Chain | Residue | Details |
D | CYS138 |
site_id | SWS_FT_FI3 |
Number of Residues | 3 |
Details | BINDING: BINDING => ECO:0000269|PubMed:31101807, ECO:0007744|PDB:6NZU |
Chain | Residue | Details |
D | ASP71 | |
D | CYS95 | |
D | CYS138 | |
A | HIS257 |
site_id | SWS_FT_FI4 |
Number of Residues | 1 |
Details | SITE: Mediates ISCU dimerization and de novo [2Fe-2S] cluster assembly => ECO:0000269|PubMed:34824239 |
Chain | Residue | Details |
D | TYR35 |
site_id | SWS_FT_FI5 |
Number of Residues | 1 |
Details | MOD_RES: Cysteine persulfide => ECO:0000250|UniProtKB:Q9D7P6 |
Chain | Residue | Details |
D | CYS69 |
site_id | SWS_FT_FI6 |
Number of Residues | 1 |
Details | MOD_RES: Cysteine persulfide => ECO:0000305|PubMed:24971490 |
Chain | Residue | Details |
D | CYS138 |
site_id | SWS_FT_FI7 |
Number of Residues | 1 |
Details | MOD_RES: Cysteine persulfide => ECO:0000305|PubMed:18650437, ECO:0000305|PubMed:23593335 |
Chain | Residue | Details |
A | CYS381 |