Research workbench
Caulobacter crescentus xylonolactonase with D-xylose
Analyse Caulobacter crescentus xylonolactonase with D-xylose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PLB
- Type
- protein
- Length
- 576 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Smp-30/CGR1 family protein
- EC
- 3.1.1.68
- UniProt
- Q9A9Z1
- Ligands
- XYP, XYS, FE2, SO4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Smp-30/CGR1 family protein (EC 3.1.1.68) | protein | 287 | 3% helix, 57% strand | Q9A9Z1 |
| B | Smp-30/CGR1 family protein (EC 3.1.1.68) | protein | 289 | 3% helix, 55% strand | Q9A9Z1 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 6 copies · chains A, B
- XYS · alpha-D-xylopyranose · sugar · chains B
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.75 | 0.94 | 31 | empty |
| 2 | 174 | 0.74 | 0.91 | 40 | empty |
| 3 | 286 | 0.69 | 0.84 | 48 | empty |
| 4 | 83 | 0.60 | 0.88 | 16 | XYP |
| 5 | 86 | 0.58 | 0.87 | 18 | XYP |
Interfaces
1 interface between chains.
- A–B · 659 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7PLB · Caulobacter crescentus xylonolactonase with D-xylose · 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 Q9A9Z1
- Elsewhere: RCSB PDB 7PLB · PDBe 7PLB · UniProt Q9A9Z1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.