Research workbench
Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1)
Analyse Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PNQ
- Type
- protein
- Length
- 764 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- [pyruvate dehydrogenase [lipoamide]]-phosphatase 1
- EC
- 3.1.3.43
- UniProt
- O88483
- Ligands
- MG
- Pockets
- 14 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | [pyruvate dehydrogenase [lipoamide]]-phosphatase 1 (EC 3.1.3.43) | protein | 382 | 39% helix, 23% strand | O88483 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.70 | 0.98 | 18 | empty |
| 2 | 61 | 0.63 | 0.93 | 24 | empty |
| 3 | 166 | 0.55 | 0.80 | 23 | empty |
| 4 | 167 | 0.54 | 0.79 | 21 | empty |
| 5 | 157 | 0.50 | 0.78 | 26 | empty |
Compared structures
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 O88483
- Elsewhere: RCSB PDB 2PNQ · PDBe 2PNQ · UniProt O88483
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