MolNFT v1 · #8095 · protein
Structure of pseudomonas cellulosa alpha-D-glucuronidase complexed with glucuronic acid and xylotriose
1GQL: “Structure of pseudomonas cellulosa alpha-D-glucuronidase complexed with glucuronic acid and xylotriose”. X-ray diffraction, 3 ligands (XYP, BDP, CO), 16 pockets (best druggability 0.85). MolNFT v1 #8095 on GenesisL1: 3D structure…
- PDB
- 1GQL
- Type
- protein
- Length
- 1,401 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-D-glucuronidase
- EC
- 3.2.1.139
- UniProt
- Q8VP74
- Ligands
- XYP, BDP, CO
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-D-glucuronidase (EC 3.2.1.139) | protein | 701 | 43% helix, 12% strand | Q8VP74 |
| B | Alpha-D-glucuronidase (EC 3.2.1.139) | protein | 700 | 43% helix, 12% strand | Q8VP74 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 4 copies · chains A, B
- BDP · beta-D-glucopyranuronic acid · sugar · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 8 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 705 | 0.85 | 0.89 | 90 | CO |
| 2 | 123 | 0.61 | 0.86 | 25 | XYP, BDP |
| 3 | 141 | 0.61 | 0.85 | 26 | XYP, BDP |
| 4 | 201 | 0.53 | 0.78 | 29 | empty |
| 5 | 152 | 0.48 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1398 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1GQL · Structure of Pseudomonas cellulosa alpha-D-glucuronidase complexed with glucuronic acid… · 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 Q8VP74
- Elsewhere: RCSB PDB 1GQL · PDBe 1GQL · UniProt Q8VP74
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