MolNFT v1 · #180005 · protein
Sugar phosphate activation of the stress sensor EIF2B
7KMF · Translation initiation factor eif-2B subunit beta: “Sugar phosphate activation of the stress sensor EIF2B”. Electron microscopy, 1 ligand (F6P), 20 pockets (best druggability 0.85). MolNFT v1 #180005 on GenesisL1: 3D structure…
- PDB
- 7KMF
- Type
- protein
- Length
- 3,005 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Translation initiation factor eif-2B subunit beta; Translation initiation factor eif-2B…
- UniProt
- P49770, Q9UI10, Q14232, Q13144, Q9NR50
- Ligands
- F6P
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 10 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Translation initiation factor eif-2B subunit beta | protein | 315 | 49% helix, 12% strand | P49770 |
| D | Translation initiation factor eif-2B subunit beta | protein | 314 | 45% helix, 13% strand | P49770 |
| F | Translation initiation factor eif-2B subunit delta | protein | 325 | 45% helix, 14% strand | Q9UI10 |
| E | Translation initiation factor eif-2B subunit delta | protein | 330 | 41% helix, 13% strand | Q9UI10 |
| H | Translation initiation factor eif-2B subunit alpha | protein | 280 | 48% helix, 15% strand | Q14232 |
| G | Translation initiation factor eif-2B subunit alpha | protein | 287 | 51% helix, 15% strand | Q14232 |
| B | Translation initiation factor eif-2B subunit epsilon | protein | 413 | 19% helix, 25% strand | Q13144 |
| I | Translation initiation factor eif-2B subunit epsilon | protein | 416 | 20% helix, 24% strand | Q13144 |
| J | Translation initiation factor eif-2B subunit gamma | protein | 162 | 20% helix, 30% strand | Q9NR50 |
| K | Translation initiation factor eif-2B subunit gamma | protein | 163 | 19% helix, 23% strand | Q9NR50 |
Ligands and binding sites
- F6P · 6-O-phosphono-beta-D-fructofuranose · ligand · 2 copies · chains H, G
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 | 623 | 0.85 | 0.90 | 110 | empty |
| 2 | 604 | 0.72 | 0.80 | 59 | empty |
| 3 | 575 | 0.72 | 0.80 | 56 | empty |
| 4 | 327 | 0.69 | 0.83 | 44 | F6P |
| 5 | 143 | 0.68 | 0.89 | 35 | empty |
Interfaces
22 interfaces between chains.
- D–E · 2087 Ų buried · 27 hydrogen bonds · protein-protein
- C–F · 2046 Ų buried · 23 hydrogen bonds · protein-protein
- H–G · 1783 Ų buried · 17 hydrogen bonds · protein-protein
- C–B · 1251 Ų buried · 8 hydrogen bonds · protein-protein
- D–I · 1220 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7KMF · Sugar phosphate activation of the stress sensor eIF2B · the same entry in another collection · chain I against I, 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 P49770
- Every structure of UniProt Q9UI10
- Every structure of UniProt Q14232
- Every structure of UniProt Q13144
- Every structure of UniProt Q9NR50
- Elsewhere: RCSB PDB 7KMF · PDBe 7KMF · UniProt P49770 · UniProt Q9UI10 · UniProt Q14232 · UniProt Q13144 · UniProt Q9NR50
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