MolNFT v1 · #35075 · protein
Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with amppnp
2E0A · Pyruvate dehydrogenase kinase isozyme 4: “Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with amppnp”. X-ray diffraction, 2 ligands (ANP, MG), 6 pockets (best druggability 0.74). MolNFT v1 #35075 on GenesisL1…
- PDB
- 2E0A
- Type
- protein
- Length
- 711 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate dehydrogenase kinase isozyme 4
- EC
- 2.7.11.2
- UniProt
- Q16654
- Ligands
- ANP, MG
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate dehydrogenase kinase isozyme 4 (EC 2.7.11.2) | protein | 358 | 52% helix, 14% strand | Q16654 |
| B | Pyruvate dehydrogenase kinase isozyme 4 (EC 2.7.11.2) | protein | 353 | 56% helix, 14% strand | Q16654 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 574 | 0.74 | 0.81 | 70 | MG, ANP |
| 2 | 532 | 0.73 | 0.81 | 69 | MG, ANP |
| 3 | 259 | 0.58 | 0.79 | 30 | empty |
| 4 | 236 | 0.49 | 0.74 | 39 | empty |
| 5 | 123 | 0.41 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1136 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2E0A · Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with AMPPNP · the same entry in another collection · chain A against A, TM-score 1.00
- Q16654 · AlphaFold monomer V2.0 prediction for [pyruvate dehydrogenase (acetyl-transferring)]… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q16654
- Elsewhere: RCSB PDB 2E0A · PDBe 2E0A · UniProt Q16654
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