MolNFT v1 · #47787 · protein
Fitted structure of adpr-EEF2 in the 80S:ADPR-EEF2:GDP:SORDARIN cryo- EM reconstruction
2P8Y · Elongation factor 2: “Fitted structure of adpr-EEF2 in the 80S:ADPR-EEF2:GDP:SORDARIN cryo- EM reconstruction”. Electron microscopy, 3 ligands (APR, SO1, GDP), 8 pockets (best druggability 0.77). MolNFT v1 #47787 on GenesisL1: 3D…
- PDB
- 2P8Y
- Type
- protein
- Length
- 814 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor 2
- UniProt
- P32324
- Ligands
- APR, SO1, GDP
- Pockets
- 8 · best druggability 0.77
Structure
electron microscopy · 1 distinct chain · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Elongation factor 2 | protein | 814 | 37% helix, 22% strand | P32324 |
Ligands and binding sites
- APR · Adenosine-5-diphosphoribose · ligand · chains T
- SO1 · [1R-(1.alpha.,3a.beta.,4.beta.,4a.beta.,7.beta.,7a.alpha.,8a.beta.)]8a-[(6-deoxy-4-O-methyl-beta-D-altropyranosyloxy)methyl]-4-formyl-4,4A,5,6,7,7A,8,8A-octahydro-7-methyl-3-(1-methylethyl)-1,4-methano-S-indacene-3A(1H)-carboxylic acid · ligand · chains T
- GDP · Guanosine-5'-diphosphate · ligand · chains T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.77 | 0.95 | 29 | empty |
| 2 | 591 | 0.76 | 0.82 | 80 | empty |
| 3 | 590 | 0.74 | 0.81 | 65 | SO1 |
| 4 | 635 | 0.68 | 0.77 | 77 | empty |
| 5 | 81 | 0.39 | 0.77 | 17 | empty |
Modifications
Observed in the structure: 4 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 2P8Y · Fitted structure of ADPR-eEF2 in the 80S:ADPR-eEF2:GDP:sordarin cryo-EM reconstruction · the same entry in another collection · chain T against T, TM-score 1.00
- 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
- Elsewhere: RCSB PDB 2P8Y · PDBe 2P8Y · UniProt P32324
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