MolNFT v1 · #60435 · protein
Crystal structure of the PDHK2-L2 complex.
3CRK · Pyruvate dehydrogenase [lipoamide] kinase isozyme 2…: “Crystal structure of the PDHK2-L2 complex.”. X-ray diffraction, 1 ligand (K), 13 pockets (best druggability 0.65). MolNFT v1 #60435 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3CRK
- Type
- protein
- Length
- 905 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate dehydrogenase [lipoamide] kinase isozyme 2, mitochondrial…
- EC
- 2.7.11.2, 2.3.1.12
- UniProt
- Q64536, P10515
- Ligands
- K
- Pockets
- 13 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate dehydrogenase [lipoamide] kinase isozyme 2, mitochondrial (EC 2.7.11.2) | protein | 370 | 51% helix, 15% strand | Q64536 |
| B | Pyruvate dehydrogenase [lipoamide] kinase isozyme 2, mitochondrial (EC 2.7.11.2) | protein | 370 | 51% helix, 15% strand | Q64536 |
| C | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial (EC 2.3.1.12) | protein | 87 | 0% helix, 45% strand | P10515 |
| D | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial (EC 2.3.1.12) | protein | 78 | 0% helix, 49% strand | P10515 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 284 | 0.65 | 0.81 | 38 | empty |
| 2 | 291 | 0.63 | 0.81 | 34 | empty |
| 3 | 237 | 0.57 | 0.78 | 40 | K |
| 4 | 208 | 0.55 | 0.79 | 29 | empty |
| 5 | 175 | 0.53 | 0.79 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2779 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 750 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 726 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 613 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 560 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 3CRK · Crystal structure of the PDHK2-L2 complex. · the same entry in another collection · chain D against D, TM-score 1.00
- Q64536 · AlphaFold monomer V2.0 prediction for [pyruvate dehydrogenase (acetyl-transferring)]… · a predicted model of the same protein · chain A against A, TM-score 0.98
- P10515 · AlphaFold monomer V2.0 prediction for dihydrolipoyllysine-residue acetyltransferase… · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q64536
- Every structure of UniProt P10515
- Elsewhere: RCSB PDB 3CRK · PDBe 3CRK · UniProt Q64536 · UniProt P10515
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