Research workbench
Electron cryo-microscopy of the eukaryotic translation initiation factor 2B from Homo sapiens
Analyse Electron cryo-microscopy of the eukaryotic translation initiation factor 2B… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CAJ
- Type
- protein
- Length
- 3,210 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Homo sapiens
- Molecule
- Translation initiation factor eIF-2B subunit epsilon; Translation initiation factor…
- UniProt
- Q13144, Q9NR50, Q14232, P49770, Q9UI10
- Ligands
- C7B
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 2.8 · 5 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Translation initiation factor eIF-2B subunit epsilon | protein | 421 | 21% helix, 25% strand | Q13144 |
| J, I | Translation initiation factor eIF-2B subunit gamma | protein | 244 | 22% helix, 22% strand | Q9NR50 |
| H, G | Translation initiation factor eIF-2B subunit alpha | protein | 265 | 46% helix, 14% strand | Q14232 |
| C, D | Translation initiation factor eIF-2B subunit beta | protein | 318 | 52% helix, 14% strand | P49770 |
| F, E | Translation initiation factor eIF-2B subunit delta | protein | 357 | 43% helix, 14% strand | Q9UI10 |
Ligands and binding sites
- C7B · 2-(4-chloranylphenoxy)-~{N}-[4-[2-(4-chloranylphenoxy) ethanoylamino]cyclohexyl]ethanamide · ligand · chains C, F, D, E
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 | 684 | 0.84 | 0.88 | 81 | empty |
| 2 | 828 | 0.84 | 0.87 | 84 | empty |
| 3 | 633 | 0.80 | 0.85 | 67 | empty |
| 4 | 417 | 0.77 | 0.86 | 58 | empty |
| 5 | 1155 | 0.77 | 0.79 | 112 | empty |
Interfaces
22 interfaces between chains.
- D–E · 2127 Ų buried · 22 hydrogen bonds · protein-protein
- C–F · 2121 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1348 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1347 Ų buried · 12 hydrogen bonds · protein-protein
- H–G · 1263 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6CAJ · Electron cryo-microscopy of the eukaryotic translation initiation factor 2B from homo… · the same entry in another collection · chain J against J, TM-score 1.00
- Q9UI10 · AlphaFold monomer V2.0 prediction for translation initiation factor eif-2B subunit delta… · a predicted model of the same protein · chain F 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 Q13144
- Every structure of UniProt Q9NR50
- Every structure of UniProt Q14232
- Every structure of UniProt P49770
- Every structure of UniProt Q9UI10
- Elsewhere: RCSB PDB 6CAJ · PDBe 6CAJ · UniProt Q13144 · UniProt Q9NR50 · UniProt Q14232 · UniProt P49770 · UniProt Q9UI10
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