MolNFT v1 · #52396 · protein
Crystal structure of amycolatopsis orientalis exo- chitosanase csxa
2VZO · Exo-beta-D-glucosaminidase: “Crystal structure of amycolatopsis orientalis exo- chitosanase csxa”. X-ray diffraction, 1 ligand (CD), 19 pockets (best druggability 0.74). MolNFT v1 #52396 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2VZO
- Type
- protein
- Length
- 1,698 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exo-beta-D-glucosaminidase
- UniProt
- Q56F26
- Ligands
- CD
- Pockets
- 19 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exo-beta-D-glucosaminidase | protein | 850 | 19% helix, 36% strand | Q56F26 |
| B | Exo-beta-D-glucosaminidase | protein | 848 | 18% helix, 37% strand | Q56F26 |
Ligands and binding sites
- CD · Cadmium ion · metal · 13 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.74 | 0.83 | 35 | CD |
| 2 | 455 | 0.73 | 0.83 | 35 | CD |
| 3 | 474 | 0.66 | 0.78 | 63 | CD |
| 4 | 310 | 0.65 | 0.81 | 48 | ACT |
| 5 | 301 | 0.64 | 0.80 | 50 | ACT |
Interfaces
1 interface between chains.
- A–B · 515 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2VZO · Crystal structure of Amycolatopsis orientalis exo-chitosanase CsxA · the same entry in another collection · chain A against A, TM-score 1.00
- Q56F26 · AlphaFold monomer V2.0 prediction for exo-beta-D-glucosaminidase (Q56F26) · a predicted model of the same protein · chain B 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 Q56F26
- Elsewhere: RCSB PDB 2VZO · PDBe 2VZO · UniProt Q56F26
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