MolNFT v1 · #34329 · protein
Crystal structure of 2-keto-3-deoxygluconate kinase from sulfolobus tokodaii complexed with 2-keto-6-phosphogluconate (alpha-furanose form)
2DCN · Hypothetical fructokinase: “Crystal structure of 2-keto-3-deoxygluconate kinase from sulfolobus tokodaii complexed with…”. X-ray diffraction, 4 ligands (CKP, ADP, MG), 20 pockets (best druggability 0.88). MolNFT v1 #34329 on…
- PDB
- 2DCN
- Type
- protein
- Length
- 3,696 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical fructokinase
- EC
- 2.7.1.45
- UniProt
- Q96XN9
- Ligands
- CKP, ADP, MG, K
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Hypothetical fructokinase (EC 2.7.1.45) | protein | 308 | 40% helix, 26% strand | Q96XN9 |
Ligands and binding sites
- CKP · 6-O-phosphono-beta-D-psicofuranosonic acid · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- ADP · Adenosine-5'-diphosphate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MG · Magnesium ion · metal · 44 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- K · Potassium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 845 | 0.88 | 0.90 | 104 | empty |
| 2 | 393 | 0.85 | 0.94 | 48 | empty |
| 3 | 378 | 0.85 | 0.94 | 45 | empty |
| 4 | 400 | 0.85 | 0.93 | 49 | empty |
| 5 | 406 | 0.85 | 0.93 | 50 | empty |
Interfaces
32 interfaces between chains.
- C–D · 1212 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1211 Ų buried · 27 hydrogen bonds · protein-protein
- K–L · 1207 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 1205 Ų buried · 25 hydrogen bonds · protein-protein
- I–J · 1205 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2DCN · Crystal structure of 2-keto-3-deoxygluconate kinase from Sulfolobus tokodaii complexed… · the same entry in another collection · chain L against L, TM-score 1.00
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 Q96XN9
- Elsewhere: RCSB PDB 2DCN · PDBe 2DCN · UniProt Q96XN9
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