Research workbench
Structure of the human frataxin-bound iron-sulfur cluster assembly complex
Analyse Structure of the human frataxin-bound iron-sulfur cluster assembly complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NZU
- Type
- protein
- Length
- 1,588 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine desulfurase, mitochondrial; Lyr motif-containing protein 4; Acyl carrier…
- EC
- 2.8.1.7, 1.16.3.1
- UniProt
- Q9Y697, Q9HD34, A0A437HBF4, Q9H1K1, Q16595
- Ligands
- PLP, 8Q1, ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Cysteine desulfurase, mitochondrial (EC 2.8.1.7) | protein | 402 | 34% helix, 14% strand | Q9Y697 |
| B, F | Lyr motif-containing protein 4 | protein | 81 | 72% helix, 1% strand | Q9HD34 |
| C, G | Acyl carrier protein | protein | 70 | 46% helix, 3% strand | A0A437HBF4 |
| D, H | Iron-sulfur cluster assembly enzyme iscu, mitochondrial | protein | 123 | 45% helix, 20% strand | Q9H1K1 |
| I, J | Frataxin, mitochondrial (EC 1.16.3.1) | protein | 118 | 29% helix, 24% strand | Q16595 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, E
- 8Q1 · S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate · ligand · 2 copies · chains A, B, C, E, F, G
- ZN · Zinc ion · metal · 2 copies · chains A, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.87 | 0.90 | 117 | PLP, ZN |
| 2 | 899 | 0.87 | 0.89 | 120 | PLP, ZN |
| 3 | 394 | 0.76 | 0.85 | 36 | 8Q1 |
| 4 | 106 | 0.75 | 0.96 | 26 | empty |
| 5 | 592 | 0.75 | 0.82 | 51 | 8Q1 |
Interfaces
18 interfaces between chains.
- A–E · 2272 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1299 Ų buried · 11 hydrogen bonds · protein-protein
- E–H · 1296 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1164 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1150 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 2 covalent (pyridoxal phosphate Schiff base, covalent ligand).
Compared structures
- 6NZU · Structure of the human frataxin-bound iron-sulfur cluster assembly complex · the same entry in another collection · chain J against J, 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 0.98
- Q16595 · AlphaFold monomer V2.0 prediction for frataxin, mitochondrial (Q16595) · a predicted model of the same protein · chain J against A, TM-score 0.98
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 A0A437HBF4
- Every structure of UniProt Q9H1K1
- Every structure of UniProt Q16595
- Elsewhere: RCSB PDB 6NZU · PDBe 6NZU · UniProt Q9Y697 · UniProt Q9HD34 · UniProt A0A437HBF4 · UniProt Q9H1K1 · UniProt Q16595
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