MolNFT v1 · #58583 · protein
Structure of the EEF2-EXOA(E546H)-NAD+ complex
3B82 · Elongation factor 2: “Structure of the EEF2-EXOA(E546H)-NAD+ complex”. X-ray diffraction, 1 ligand (NAD), 20 pockets (best druggability 0.82). MolNFT v1 #58583 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3B82
- Type
- protein
- Length
- 3,090 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Elongation factor 2; Exotoxin a
- EC
- 2.4.2.36
- UniProt
- P32324, P11439
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Elongation factor 2 | protein | 823 | 37% helix, 26% strand | P32324 |
| B, D, F | Exotoxin a (EC 2.4.2.36) | protein | 207 | 29% helix, 21% strand | P11439 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1040 | 0.82 | 0.83 | 96 | empty |
| 2 | 889 | 0.81 | 0.83 | 86 | empty |
| 3 | 897 | 0.81 | 0.83 | 73 | empty |
| 4 | 912 | 0.79 | 0.82 | 112 | empty |
| 5 | 733 | 0.76 | 0.81 | 91 | empty |
Interfaces
6 interfaces between chains.
- E–F · 986 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 986 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 847 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 340 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 333 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (nonstandard).
Compared structures
- 3B82 · Structure of the eEF2-ExoA(E546H)-NAD+ complex · the same entry in another collection · chain F against F, TM-score 1.00
- P11439 · AlphaFold monomer V2.0 prediction for exotoxin a (P11439) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P32324 · AlphaFold monomer V2.0 prediction for elongation factor 2 (P32324) · a predicted model of the same protein · chain C 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 P11439
- Elsewhere: RCSB PDB 3B82 · PDBe 3B82 · UniProt P32324 · UniProt P11439
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