Research workbench
Structure of the eEF2-ExoA(E546A)-NAD+ complex
Analyse Structure of the eEF2-ExoA(E546A)-NAD+ complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B8H
- Type
- protein
- Length
- 3,090 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Pseudomonas aeruginosa; Saccharomyces cerevisiae
- Molecule
- Elongation factor 2; Exotoxin A
- EC
- 2.4.2.36
- UniProt
- P32324, P11439
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.5 · 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 | 28% 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.81 | 0.82 | 99 | empty |
| 2 | 1020 | 0.80 | 0.81 | 81 | empty |
| 3 | 937 | 0.79 | 0.81 | 112 | empty |
| 4 | 491 | 0.77 | 0.85 | 53 | empty |
| 5 | 1026 | 0.77 | 0.79 | 112 | empty |
Interfaces
6 interfaces between chains.
- E–F · 986 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 977 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 798 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 331 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 328 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (nonstandard).
Compared structures
- 3B8H · Structure of the EEF2-EXOA(E546A)-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 0.66
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 3B8H · PDBe 3B8H · UniProt P32324 · UniProt P11439
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