MolNFT v1 · #34509 · protein
R337A mutant of pyruvate phosphate dikinase
2DIK · Protein (pyruvate phosphate dikinase): “R337A mutant of pyruvate phosphate dikinase”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.86). MolNFT v1 #34509 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2DIK
- Type
- protein
- Length
- 869 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (pyruvate phosphate dikinase)
- EC
- 2.7.9.1
- UniProt
- P22983
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (pyruvate phosphate dikinase) (EC 2.7.9.1) | protein | 869 | 47% helix, 16% strand | P22983 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.86 | 0.87 | 144 | empty |
| 2 | 199 | 0.46 | 0.75 | 30 | SO4 |
| 3 | 75 | 0.37 | 0.76 | 18 | empty |
| 4 | 58 | 0.36 | 0.79 | 16 | empty |
| 5 | 53 | 0.29 | 0.75 | 14 | 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 P22983
- Elsewhere: RCSB PDB 2DIK · PDBe 2DIK · UniProt P22983
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