Research workbench
Iron and selenomethionine containing iron sulfur cluster repair protein ytfe
Analyse Iron and selenomethionine containing iron sulfur cluster repair protein ytfe in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FNN
- Type
- protein
- Length
- 427 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
- FE2, FE, CL, O
- Pockets
- 4 · best druggability 0.51
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 | 208 | 73% helix, 1% strand | P69506 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 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 | 127 | 0.51 | 0.80 | 23 | empty |
| 2 | 154 | 0.49 | 0.78 | 20 | empty |
| 3 | 97 | 0.41 | 0.77 | 18 | empty |
| 4 | 54 | 0.40 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 512 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 5FNN · Iron and Selenomethionine 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 5FNN · PDBe 5FNN · UniProt P69506
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