MolNFT v1 · #52401 · protein
Complex of amycolatopsis orientalis exo-chitosanase csxa E541A with pnp-beta-D-glucosamine
2VZT · Exo-beta-D-glucosaminidase: “Complex of amycolatopsis orientalis exo-chitosanase csxa E541A with pnp-beta-D-glucosamine”. X-ray diffraction, 2 ligands (PNJ, CD), 17 pockets (best druggability 0.78). MolNFT v1 #52401 on GenesisL1: 3D…
- PDB
- 2VZT
- Type
- protein
- Length
- 1,700 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exo-beta-D-glucosaminidase
- UniProt
- Q56F26
- Ligands
- PNJ, CD
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Exo-beta-D-glucosaminidase | protein | 850 | 18% helix, 36% strand | Q56F26 |
Ligands and binding sites
- PNJ · 4-nitrophenyl 2-amino-2-deoxy-beta-D-glucopyranoside · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 6 copies · chains A, B
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.78 | 0.81 | 93 | empty |
| 2 | 493 | 0.73 | 0.83 | 35 | empty |
| 3 | 344 | 0.66 | 0.81 | 56 | empty |
| 4 | 276 | 0.63 | 0.81 | 51 | ACT |
| 5 | 240 | 0.62 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 495 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2VZT · Complex of Amycolatopsis orientalis exo-chitosanase CsxA E541A with PNP-beta-D-glucosamine · 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 2VZT · PDBe 2VZT · UniProt Q56F26
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