MolNFT v1 · #168500 · protein
N-terminal mutation of ISCU2 (L35H36) traps NFS1 cys loop in the active site of ISCU2 without metal present. structure of human mitochondrial complex NFS1-ISCU2(L35H36)-ISD11 with E.COLI ACP1 at 1.9 a resolution (NIAU)2.
6WIH · Cysteine desulfurase, mitochondrial: “N-terminal mutation of ISCU2 (L35H36) traps NFS1 cys loop in the active site of ISCU2 without metal present.…”. X-ray diffraction, 4 ligands (PLP, P15, EDT), 8 pockets (best druggability 0.73).…
- PDB
- 6WIH
- Type
- protein
- Length
- 685 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine desulfurase, mitochondrial; Lyr motif-containing protein 4; Acyl carrier…
- EC
- 2.8.1.7
- UniProt
- Q9Y697, Q9HD34, B7MJ81, Q9H1K1
- Ligands
- PLP, P15, EDT, 8Q1
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine desulfurase, mitochondrial (EC 2.8.1.7) | protein | 401 | 43% helix, 15% strand | Q9Y697 |
| B | Lyr motif-containing protein 4 | protein | 84 | 75% helix, 1% strand | Q9HD34 |
| C | Acyl carrier protein | protein | 75 | 55% helix, 3% strand | B7MJ81 |
| D | Iron-sulfur cluster assembly enzyme iscu, mitochondrial | protein | 125 | 49% helix, 23% strand | Q9H1K1 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- P15 · 2,5,8,11,14,17-hexaoxanonadecan-19-ol · ligand · chains A, D
- EDT · {[-(bis-carboxymethyl-amino)-ethyl]-carboxymethyl-amino}-acetic acid · ligand · chains A, B
- 8Q1 · S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate · ligand · chains A, B, C
- EDO · 1,2-ethanediol · additive · 38 copies · chains A, D, B, C
- PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B, D
- PGE · Triethylene glycol · additive · 3 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A
- 1PE · Pentaethylene glycol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.73 | 0.82 | 52 | PGE, EDO, 8Q1 |
| 2 | 328 | 0.61 | 0.78 | 36 | EDO |
| 3 | 202 | 0.52 | 0.78 | 25 | empty |
| 4 | 142 | 0.46 | 0.77 | 17 | empty |
| 5 | 181 | 0.46 | 0.74 | 23 | GOL |
Interfaces
3 interfaces between chains.
- A–D · 1177 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1139 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 549 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor, 1 covalent (pyridoxal phosphate Schiff base, covalent ligand).
Compared structures
- 6WIH · N-terminal mutation of ISCU2 (L35H36) traps Nfs1 Cys loop in the active site of ISCU2… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9Y697 · AlphaFold monomer V2.0 prediction for cysteine desulfurase, mitochondrial (Q9Y697) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9H1K1 · AlphaFold monomer V2.0 prediction for iron-sulfur cluster assembly enzyme iscu… · a predicted model of the same protein · chain D against A, TM-score 0.98
- Q9HD34 · AlphaFold monomer V2.0 prediction for lyr motif-containing protein 4 (Q9HD34) · a predicted model of the same protein · chain B against A, TM-score 0.97
- B7MJ81 · AlphaFold monomer V2.0 prediction for acyl carrier protein (B7MJ81) · a predicted model of the same protein · chain C against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9Y697
- Every structure of UniProt Q9HD34
- Every structure of UniProt B7MJ81
- Every structure of UniProt Q9H1K1
- Elsewhere: RCSB PDB 6WIH · PDBe 6WIH · UniProt Q9Y697 · UniProt Q9HD34 · UniProt B7MJ81 · UniProt Q9H1K1
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