Research workbench
Core-binding domain of fungal E3-binding domain bound to the pyruvate dehydrogenase E2 core
Analyse Core-binding domain of fungal E3-binding domain bound to the pyruvate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7R5M
- Type
- protein
- Length
- 1,491 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.3
- Source
- Neurospora crassa
- Molecule
- Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase…
- EC
- 2.3.1.12
- UniProt
- P20285, Q7RWS2
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · resolution 3.3 · 3 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial (EC 2.3.1.12) | protein | 233 | 36% helix, 29% strand | P20285 |
| F, J, M | Pyruvate dehydrogenase X component | protein | 120 | 45% helix, 13% strand | Q7RWS2 |
| H, K, L | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial (EC 2.3.1.12) | protein | 144 | 39% helix, 25% strand | P20285 |
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.82 | 0.83 | 87 | empty |
| 2 | 242 | 0.79 | 0.91 | 29 | empty |
| 3 | 660 | 0.74 | 0.80 | 75 | empty |
| 4 | 698 | 0.74 | 0.79 | 84 | empty |
| 5 | 653 | 0.74 | 0.80 | 79 | empty |
Interfaces
15 interfaces between chains.
- A–B · 1371 Ų buried · 12 hydrogen bonds · protein-protein
- B–G · 1366 Ų buried · 14 hydrogen bonds · protein-protein
- A–G · 1362 Ų buried · 11 hydrogen bonds · protein-protein
- A–L · 795 Ų buried · 0 hydrogen bonds · protein-protein
- B–K · 782 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- P20285 · AlphaFold monomer V2.0 prediction for dihydrolipoyllysine-residue acetyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P20285
- Every structure of UniProt Q7RWS2
- Elsewhere: RCSB PDB 7R5M · PDBe 7R5M · UniProt P20285 · UniProt Q7RWS2
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