MolNFT v1 · #69781 · protein
The crystal structure of xlylulose kinase from yersinia pseudotuberculosis
3L0Q · Xylulose kinase: “The crystal structure of xlylulose kinase from yersinia pseudotuberculosis”. X-ray diffraction, 1 ligand (XUL), 11 pockets (best druggability 0.71). MolNFT v1 #69781 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3L0Q
- Type
- protein
- Length
- 1,083 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylulose kinase
- UniProt
- Q665C6
- Ligands
- XUL
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylulose kinase | protein | 541 | 43% helix, 21% strand | Q665C6 |
| B | Xylulose kinase | protein | 542 | 42% helix, 19% strand | Q665C6 |
Ligands and binding sites
- XUL · D-xylulose · ligand · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
- GOL · Glycerol · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.71 | 0.78 | 90 | XUL |
| 2 | 646 | 0.70 | 0.78 | 60 | EPE |
| 3 | 171 | 0.49 | 0.77 | 20 | empty |
| 4 | 69 | 0.45 | 0.82 | 12 | empty |
| 5 | 185 | 0.44 | 0.74 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 739 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered).
Compared structures
- 3L0Q · The crystal structure of xlylulose kinase from Yersinia pseudotuberculosis · 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 Q665C6
- Elsewhere: RCSB PDB 3L0Q · PDBe 3L0Q · UniProt Q665C6
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