MolNFT v1 · #39714 · protein
Crystal structure of an EIF4G-like protein from danio rerio
2I2O: “Crystal structure of an EIF4G-like protein from danio rerio”. X-ray diffraction, 1 ligand (NI), 2 pockets (best druggability 0.42). MolNFT v1 #39714 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2I2O
- Type
- protein
- Length
- 421 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EIF4G-like protein
- UniProt
- Q5EAQ1
- Ligands
- NI
- Pockets
- 2 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | EIF4G-like protein | protein | 211 | 78% helix, 1% strand | Q5EAQ1 |
| B | EIF4G-like protein | protein | 210 | 78% helix, 1% strand | Q5EAQ1 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.42 | 0.81 | 19 | empty |
| 2 | 62 | 0.37 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 935 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 2I2O · Crystal Structure of an eIF4G-like Protein from Danio rerio · the same entry in another collection · chain B against B, TM-score 1.00
- Q5EAQ1 · AlphaFold monomer V2.0 prediction for MIF4G domain-containing protein B (Q5EAQ1) · a predicted model of the same protein · chain B 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 Q5EAQ1
- Elsewhere: RCSB PDB 2I2O · PDBe 2I2O · UniProt Q5EAQ1
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