MolNFT v1 · #112453 · protein
Lipomyces starkeyi levoglucosan kinase bound to levoglucosan, ADP and magnesium.
4ZLU: “Lipomyces starkeyi levoglucosan kinase bound to levoglucosan, ADP and magnesium.”. X-ray diffraction, 3 ligands (ADP, 4PW, MG), 11 pockets (best druggability 0.78). MolNFT v1 #112453 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4ZLU
- Type
- protein
- Length
- 865 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Levoglucosan kinase
- EC
- 2.7.-.-
- UniProt
- B3VI55
- Ligands
- ADP, 4PW, MG
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Levoglucosan kinase (EC 2.7.-.-) | protein | 432 | 41% helix, 22% strand | B3VI55 |
| B | Levoglucosan kinase (EC 2.7.-.-) | protein | 433 | 41% helix, 22% strand | B3VI55 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- 4PW · Levoglucosan · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.78 | 0.98 | 26 | empty |
| 2 | 562 | 0.76 | 0.83 | 69 | ADP, 4PW |
| 3 | 373 | 0.75 | 0.86 | 57 | ADP, 4PW, MG |
| 4 | 53 | 0.70 | 0.98 | 23 | empty |
| 5 | 99 | 0.54 | 0.84 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2391 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 4ZLU · Lipomyces starkeyi levoglucosan kinase bound to levoglucosan, ADP and magnesium. · 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 4ZLU · PDBe 4ZLU · UniProt B3VI55
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