Research workbench
Architecture of the human mitochondrial iron-sulfur cluster assembly machinery: the complex formed by the iron donor, the sulfur donor, and the scaffold
Analyse Architecture of the human mitochondrial iron-sulfur cluster assembly machinery… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KZ5
- Type
- protein
- Length
- 8,136 residues
- Chains
- 36
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine desulfurase, mitochondrial; Frataxin, mitochondrial; Iron-sulfur cluster…
- EC
- 2.8.1.7, 1.16.3.1
- UniProt
- Q9Y697, Q16595, Q9H1K1
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 3 distinct chains · 36% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1, 2, 3, 4, M, N, O, P, Q, R, S, T | Cysteine desulfurase, mitochondrial (EC 2.8.1.7) | protein | 391 | 39% helix, 9% strand | Q9Y697 |
| A, B, C, D, E, F, G, H, I, J, K, L | Frataxin, mitochondrial (EC 1.16.3.1) | protein | 169 | 25% helix, 8% strand | Q16595 |
| a, b, c, d, e, f, g, h, i, j, k, l | Iron-sulfur cluster assembly enzyme iscu, mitochondrial | protein | 118 | 44% helix, 9% strand | Q9H1K1 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.90 | 0.92 | 130 | empty |
| 2 | 1134 | 0.90 | 0.92 | 120 | empty |
| 3 | 1155 | 0.89 | 0.91 | 171 | empty |
| 4 | 509 | 0.89 | 0.95 | 80 | empty |
| 5 | 1010 | 0.89 | 0.90 | 92 | empty |
Interfaces
195 interfaces between chains.
- 4–D · 2581 Ų buried · 33 hydrogen bonds · protein-protein
- T–H · 2383 Ų buried · 21 hydrogen bonds · protein-protein
- 1–4 · 2344 Ų buried · 50 hydrogen bonds · protein-protein
- Q–K · 2335 Ų buried · 24 hydrogen bonds · protein-protein
- 2–J · 2248 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- Q9Y697 · AlphaFold monomer V2.0 prediction for cysteine desulfurase, mitochondrial (Q9Y697) · a predicted model of the same protein · chain 1 against A, TM-score 0.72
- Q16595 · AlphaFold monomer V2.0 prediction for frataxin, mitochondrial (Q16595) · a predicted model of the same protein · chain E against A, TM-score 0.71
- Q9H1K1 · AlphaFold monomer V2.0 prediction for iron-sulfur cluster assembly enzyme iscu… · a predicted model of the same protein · chain a against A, TM-score 0.70
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 Q16595
- Every structure of UniProt Q9H1K1
- Elsewhere: RCSB PDB 5KZ5 · PDBe 5KZ5 · UniProt Q9Y697 · UniProt Q16595 · UniProt Q9H1K1
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