Research workbench
Crystal structure of the asymmetric PDK3-L2 complex
Analyse Crystal structure of the asymmetric PDK3-L2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PNR
- Type
- protein
- Length
- 1,588 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- [pyruvate dehydrogenase [lipoamide]] kinase isozyme 3; Dihydrolipoyllysine-residue…
- EC
- 2.7.11.2, 2.3.1.12
- UniProt
- Q15120, P10515
- Ligands
- RED
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | [pyruvate dehydrogenase [lipoamide]] kinase isozyme 3 (EC 2.7.11.2) | protein | 374 | 53% helix, 14% strand | Q15120 |
| B, F | [pyruvate dehydrogenase [lipoamide]] kinase isozyme 3 (EC 2.7.11.2) | protein | 341 | 52% helix, 16% strand | Q15120 |
| C, G | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12) | protein | 79 | 0% helix, 42% strand | P10515 |
Ligands and binding sites
- RED · Dihydrolipoic acid · ligand · 2 copies · chains A, B, C, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.70 | 0.88 | 26 | RED |
| 2 | 190 | 0.67 | 0.85 | 23 | RED |
| 3 | 407 | 0.67 | 0.80 | 52 | empty |
| 4 | 383 | 0.61 | 0.77 | 46 | empty |
| 5 | 237 | 0.60 | 0.80 | 23 | empty |
Interfaces
8 interfaces between chains.
- E–F · 2343 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 2254 Ų buried · 43 hydrogen bonds · protein-protein
- E–G · 559 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 536 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 513 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2PNR · Crystal Structure of the asymmetric Pdk3-l2 Complex · the same entry in another collection · chain G against G, TM-score 1.00
- Q15120 · AlphaFold monomer V2.0 prediction for [pyruvate dehydrogenase (acetyl-transferring)]… · a predicted model of the same protein · chain B against A, TM-score 0.98
- P10515 · AlphaFold monomer V2.0 prediction for dihydrolipoyllysine-residue acetyltransferase… · a predicted model of the same protein · chain C 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 Q15120
- Every structure of UniProt P10515
- Elsewhere: RCSB PDB 2PNR · PDBe 2PNR · UniProt Q15120 · UniProt P10515
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