MolNFT v1 · #46122 · protein
2-keto-3-deoxygluconate aldolase from sulfolobus acidocaldarius in complex with pyruvate
2NUY · 2-keto-3-DEOXYGLUCONATE/2-keto-3-deoxy-6-phospho gluconate…: “2-keto-3-deoxygluconate aldolase from sulfolobus acidocaldarius in complex with pyruvate”. X-ray diffraction, 2 ligands (PYR, MG), 7 pockets (best druggability 0.75).…
- PDB
- 2NUY
- Type
- protein
- Length
- 576 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-keto-3-DEOXYGLUCONATE/2-keto-3-deoxy-6-phospho gluconate aldolase
- EC
- 4.1.2.14
- UniProt
- Q4JC35
- Ligands
- PYR, MG
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-keto-3-DEOXYGLUCONATE/2-keto-3-deoxy-6-phospho gluconate aldolase (EC 4.1.2.14) | protein | 288 | 52% helix, 14% strand | Q4JC35 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.75 | 0.91 | 30 | PYR |
| 2 | 222 | 0.71 | 0.87 | 33 | PYR |
| 3 | 255 | 0.67 | 0.84 | 35 | empty |
| 4 | 97 | 0.36 | 0.74 | 18 | empty |
| 5 | 91 | 0.36 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1867 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2NUY · 2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius in complex with pyruvate · the same entry in another collection · chain A against A, TM-score 1.00
- Q4JC35 · AlphaFold monomer V2.0 prediction for 2-dehydro-3-deoxy… · a predicted model of the same protein · chain A 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 Q4JC35
- Elsewhere: RCSB PDB 2NUY · PDBe 2NUY · UniProt Q4JC35
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