Research workbench
Low solvent content crystal form of zn containing iron sulfur cluster repair protein ytfe
Analyse Low solvent content crystal form of zn containing iron sulfur cluster repair… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FNY
- Type
- protein
- Length
- 437 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, FE, O
- Pockets
- 4 · best druggability 0.71
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 | 218 | 72% helix, 1% strand | P69506 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A, B
- FE · Fe (III) ion · metal · chains B
- O · Oxygen atom · ion · 2 copies · chains A, B
- 2PE · Nonaethylene glycol · additive · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 778 | 0.71 | 0.77 | 71 | empty |
| 2 | 459 | 0.68 | 0.79 | 40 | empty |
| 3 | 289 | 0.57 | 0.77 | 32 | empty |
| 4 | 52 | 0.49 | 0.87 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 530 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5FNY · Low solvent content crystal form of 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 A against A, TM-score 1.00
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 5FNY · PDBe 5FNY · UniProt P69506
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