Research workbench
2-keto-3-deoxygluconate aldolase from sulfolobus acidocaldarius, native structure at 1.8 a resolution
Analyse 2-keto-3-deoxygluconate aldolase from sulfolobus acidocaldarius, native… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NUW
- 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
- MG
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 13% 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 | 51% helix, 13% strand | Q4JC35 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
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 | 205 | 0.75 | 0.90 | 32 | empty |
| 2 | 241 | 0.73 | 0.88 | 32 | empty |
| 3 | 257 | 0.68 | 0.85 | 34 | empty |
| 4 | 97 | 0.36 | 0.74 | 17 | empty |
| 5 | 93 | 0.36 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1806 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2NUW · 2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius, native structure at 1.8… · 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 2NUW · PDBe 2NUW · UniProt Q4JC35
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