Research workbench
Structure of pseudomonas cellulosa alpha-D-glucuronidase complexed with glucuronic acid
Analyse Structure of pseudomonas cellulosa alpha-D-glucuronidase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GQK
- Type
- protein
- Length
- 1,416 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
- BDP, CO
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-D-glucuronidase (EC 3.2.1.139) | protein | 708 | 42% helix, 12% strand | Q8VP74 |
Ligands and binding sites
- 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 · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.85 | 0.89 | 88 | EDO, CO |
| 2 | 127 | 0.56 | 0.83 | 25 | BDP |
| 3 | 275 | 0.56 | 0.77 | 36 | empty |
| 4 | 136 | 0.54 | 0.82 | 26 | BDP |
| 5 | 206 | 0.51 | 0.77 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2051 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 1GQK · 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 1GQK · PDBe 1GQK · UniProt Q8VP74
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