Research workbench
Structure of the EEF2-EXOA(R551H)-NAD+ complex
Analyse Structure of the EEF2-EXOA(R551H)-NAD+ complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B78
- 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.-
- UniProt
- P32324, P11439
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.81
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.-) | protein | 207 | 28% helix, 21% strand | P11439 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains B, C, D, 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 | 970 | 0.81 | 0.83 | 85 | empty |
| 2 | 1077 | 0.80 | 0.81 | 93 | empty |
| 3 | 905 | 0.78 | 0.81 | 114 | empty |
| 4 | 1167 | 0.77 | 0.79 | 131 | empty |
| 5 | 477 | 0.76 | 0.84 | 60 | empty |
Interfaces
6 interfaces between chains.
- C–D · 969 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 915 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 768 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 344 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 338 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (nonstandard).
Compared structures
- 3B78 · Structure of the eEF2-ExoA(R551H)-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 3B78 · PDBe 3B78 · UniProt P32324 · UniProt P11439
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