MolNFT v1 · #33305 · protein
Crystal structure of L-rhamnulose kinase from escherichia COLI in an open uncomplexed conformation.
2CGK: “Crystal structure of L-rhamnulose kinase from escherichia COLI in an open uncomplexed conformation.”. X-ray diffraction, 6 pockets (best druggability 0.78). MolNFT v1 #33305 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2CGK
- Type
- protein
- Length
- 956 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-rhamnulose kinase
- EC
- 2.7.1.5
- UniProt
- Q8X899
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | L-rhamnulose kinase (EC 2.7.1.5) | protein | 478 | 41% helix, 21% strand | Q8X899 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.78 | 0.81 | 72 | empty |
| 2 | 887 | 0.77 | 0.80 | 73 | empty |
| 3 | 93 | 0.37 | 0.75 | 25 | empty |
| 4 | 70 | 0.34 | 0.76 | 21 | empty |
| 5 | 55 | 0.33 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 326 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2CGK · Crystal Structure of L-rhamnulose kinase from Escherichia coli in an open uncomplexed… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8X899 · AlphaFold monomer V2.0 prediction for rhamnulokinase (Q8X899) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q8X899
- Elsewhere: RCSB PDB 2CGK · PDBe 2CGK · UniProt Q8X899
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