Research workbench
C-terminal CBM35 from amycolatopsis orientalis exo-chitosanase csxa in complex with glucuronic acid
Analyse C-terminal CBM35 from amycolatopsis orientalis exo-chitosanase csxa in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VZR
- Type
- protein
- Length
- 251 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exo-beta-D-glucosaminidase
- UniProt
- Q56F26
- Ligands
- GCU, CA
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exo-beta-D-glucosaminidase | protein | 125 | 2% helix, 54% strand | Q56F26 |
| B | Exo-beta-D-glucosaminidase | protein | 126 | 2% helix, 57% strand | Q56F26 |
Ligands and binding sites
- GCU · alpha-D-glucopyranuronic acid · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.48 | 0.75 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 204 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2VZR · C-terminal CBM35 from Amycolatopsis orientalis exo-chitosanase CsxA in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
- Q56F26 · AlphaFold monomer V2.0 prediction for exo-beta-D-glucosaminidase (Q56F26) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q56F26
- Elsewhere: RCSB PDB 2VZR · PDBe 2VZR · UniProt Q56F26
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