MolNFT v1 · #47785 · protein
Fitted structure of EEF2 in the 80S:EEF2:GDPNP cryo-EM reconstruction
2P8W · Elongation factor 2: “Fitted structure of EEF2 in the 80S:EEF2:GDPNP cryo-EM reconstruction”. Electron microscopy, 1 ligand (GNP), 12 pockets (best druggability 0.78). MolNFT v1 #47785 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2P8W
- Type
- protein
- Length
- 849 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor 2; Elongation factor tu-B
- UniProt
- P32324, P60339
- Ligands
- GNP
- Pockets
- 12 · best druggability 0.78
Structure
electron microscopy · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Elongation factor 2 | protein | 814 | 37% helix, 23% strand | P32324 |
| S | Elongation factor tu-B | protein | 35 | 26% helix, 9% strand | P60339 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains T, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.78 | 0.94 | 28 | empty |
| 2 | 940 | 0.76 | 0.79 | 86 | empty |
| 3 | 270 | 0.72 | 0.85 | 42 | empty |
| 4 | 717 | 0.71 | 0.77 | 66 | empty |
| 5 | 151 | 0.66 | 0.87 | 43 | GNP |
Interfaces
1 interface between chains.
- T–S · 1522 Ų buried · 74 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent, 1 isopeptide (covalent ligand, isopeptide).
Compared structures
- 2P8W · Fitted structure of eEF2 in the 80S:eEF2:GDPNP cryo-EM reconstruction · the same entry in another collection · chain T against T, TM-score 1.00
- P60339 · AlphaFold monomer V2.0 prediction for elongation factor tu-B (P60339) · a predicted model of the same protein · chain S against A, TM-score 0.91
- P32324 · AlphaFold monomer V2.0 prediction for elongation factor 2 (P32324) · a predicted model of the same protein · chain T against A, TM-score 0.67
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 P32324
- Every structure of UniProt P60339
- Elsewhere: RCSB PDB 2P8W · PDBe 2P8W · UniProt P32324 · UniProt P60339
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