MolNFT v1 · #47788 · protein
Fitted structure of adpr-EEF2 in the 80S:ADPR-EEF2:GDPNP:SORDARIN cryo-EM reconstruction
2P8Z · Elongation factor 2: “Fitted structure of adpr-EEF2 in the 80S:ADPR-EEF2:GDPNP:SORDARIN cryo-EM reconstruction”. Electron microscopy, 3 ligands (APR, SO1, GNP), 10 pockets (best druggability 0.76). MolNFT v1 #47788 on GenesisL1: 3D…
- PDB
- 2P8Z
- 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
- APR, SO1, GNP
- Pockets
- 10 · best druggability 0.76
Structure
electron microscopy · 2 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Elongation factor 2 | protein | 814 | 37% helix, 24% strand | P32324 |
| S | Elongation factor tu-B | protein | 35 | 26% helix, 9% strand | P60339 |
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
- 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
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.76 | 0.80 | 75 | empty |
| 2 | 632 | 0.73 | 0.80 | 57 | SO1 |
| 3 | 156 | 0.69 | 0.88 | 44 | GNP |
| 4 | 235 | 0.53 | 0.76 | 34 | empty |
| 5 | 93 | 0.39 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- T–S · 1532 Ų buried · 75 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 2P8Z · Fitted structure of ADPR-eEF2 in the 80S:ADPR-eEF2:GDPNP:sordarin 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 0.71
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 2P8Z · PDBe 2P8Z · UniProt P32324 · UniProt P60339
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