MolNFT v1 · #134968 · protein
Crystal structure of a lipomyces starkeyi levoglucosan kinase G359R mutant
5TKR: “Crystal structure of a lipomyces starkeyi levoglucosan kinase G359R mutant”. X-ray diffraction, 4 ligands (ADP, MG, K), 5 pockets (best druggability 0.78). MolNFT v1 #134968 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5TKR
- Type
- protein
- Length
- 432 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Levoglucosan kinase
- EC
- 2.7.-.-
- UniProt
- B3VI55
- Ligands
- ADP, MG, K, SO4
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Levoglucosan kinase (EC 2.7.-.-) | protein | 432 | 40% helix, 22% strand | B3VI55 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- K · Potassium ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.78 | 0.89 | 52 | ADP, MG, SO4, K |
| 2 | 55 | 0.72 | 0.99 | 23 | empty |
| 3 | 99 | 0.38 | 0.76 | 17 | empty |
| 4 | 75 | 0.38 | 0.78 | 16 | empty |
| 5 | 62 | 0.37 | 0.79 | 13 | K |
Compared structures
- 5TKR · Crystal structure of a Lipomyces starkeyi levoglucosan kinase G359R mutant · the same entry in another collection · chain A against A, 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 B3VI55
- Elsewhere: RCSB PDB 5TKR · PDBe 5TKR · UniProt B3VI55
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