MolNFT v1 · #119160 · protein
High resolution zn containing iron sulfur cluster repair protein ytfe
5FNP · Iron-sulfur cluster repair protein ytfe: “High resolution zn containing iron sulfur cluster repair protein ytfe”. X-ray diffraction, 3 ligands (ZN, CL, O), 4 pockets (best druggability 0.52). MolNFT v1 #119160 on GenesisL1: 3D…
- PDB
- 5FNP
- Type
- protein
- Length
- 429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iron-sulfur cluster repair protein ytfe
- EC
- 1.7.2.5
- UniProt
- P69506
- Ligands
- ZN, CL, O
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iron-sulfur cluster repair protein ytfe (EC 1.7.2.5) | protein | 219 | 74% helix, 1% strand | P69506 |
| B | Iron-sulfur cluster repair protein ytfe (EC 1.7.2.5) | protein | 210 | 72% helix, 1% strand | P69506 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- O · Oxygen atom · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.52 | 0.87 | 18 | empty |
| 2 | 145 | 0.48 | 0.78 | 22 | empty |
| 3 | 58 | 0.46 | 0.84 | 18 | empty |
| 4 | 130 | 0.44 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 189 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5FNP · High resolution Zn containing Iron sulfur cluster repair protein YtfE · the same entry in another collection · chain A against A, TM-score 1.00
- P69506 · AlphaFold monomer V2.0 prediction for iron-sulfur cluster repair protein ytfe (P69506) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P69506
- Elsewhere: RCSB PDB 5FNP · PDBe 5FNP · UniProt P69506
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