MolNFT v1 · #148195 · protein
Eukaryotic initiation factor EIF2B in complex with isrib
6EZO · Translation initiation factor eif-2B subunit alpha: “Eukaryotic initiation factor EIF2B in complex with isrib”. Electron microscopy, 1 ligand (C7B), 20 pockets (best druggability 0.88). MolNFT v1 #148195 on GenesisL1: 3D structure…
- PDB
- 6EZO
- Type
- protein
- Length
- 3,367 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Translation initiation factor eif-2B subunit alpha; Translation initiation factor eif-2B…
- UniProt
- Q14232, P49770, Q9NR50, Q9UI10, Q13144
- Ligands
- C7B
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 8 distinct chains · 27% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Translation initiation factor eif-2B subunit alpha | protein | 280 | 43% helix, 14% strand | Q14232 |
| C | Translation initiation factor eif-2B subunit beta | protein | 307 | 37% helix, 11% strand | P49770 |
| D | Translation initiation factor eif-2B subunit beta | protein | 308 | 37% helix, 10% strand | P49770 |
| E, F | Translation initiation factor eif-2B subunit gamma | protein | 347 | 9% helix, 14% strand | Q9NR50 |
| G | Translation initiation factor eif-2B subunit delta | protein | 355 | 29% helix, 7% strand | Q9UI10 |
| H | Translation initiation factor eif-2B subunit delta | protein | 353 | 29% helix, 8% strand | Q9UI10 |
| I | Human eukaryotic initiation factor EIF2B epsilon subunits | protein | 396 | 18% helix, 12% strand | Q13144 |
| J | Human eukaryotic initiation factor EIF2B epsilon subunits | protein | 394 | 18% helix, 13% strand | Q13144 |
Ligands and binding sites
- C7B · 2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy) ethanoylamino]cyclohexyl]ethanamide · ligand · chains C, D, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 826 | 0.88 | 0.91 | 169 | C7B |
| 2 | 1013 | 0.87 | 0.89 | 167 | empty |
| 3 | 943 | 0.87 | 0.89 | 143 | empty |
| 4 | 722 | 0.82 | 0.86 | 107 | empty |
| 5 | 597 | 0.82 | 0.87 | 109 | empty |
Interfaces
18 interfaces between chains.
- C–G · 1450 Ų buried · 7 hydrogen bonds · protein-protein
- D–H · 1395 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 978 Ų buried · 2 hydrogen bonds · protein-protein
- C–I · 670 Ų buried · 4 hydrogen bonds · protein-protein
- D–J · 526 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6EZO · Eukaryotic initiation factor EIF2B in complex with ISRIB · the same entry in another collection · chain J against J, TM-score 1.00
- Q13144 · AlphaFold monomer V2.0 prediction for translation initiation factor eif-2B subunit… · a predicted model of the same protein · chain I against A, TM-score 0.97
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 Q14232
- Every structure of UniProt P49770
- Every structure of UniProt Q9NR50
- Every structure of UniProt Q9UI10
- Every structure of UniProt Q13144
- Elsewhere: RCSB PDB 6EZO · PDBe 6EZO · UniProt Q14232 · UniProt P49770 · UniProt Q9NR50 · UniProt Q9UI10 · UniProt Q13144
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