MolNFT v1 · #148200 · protein
Crystal structure of GH20 exo beta-N-acetylglucosaminidase D437A inactive mutant from vibrio harveyi
6EZT · Beta-N-acetylglucosaminidase NAG2: “Crystal structure of GH20 exo beta-N-acetylglucosaminidase D437A inactive mutant from vibrio harveyi”. X-ray diffraction, 19 pockets (best druggability 0.81). MolNFT v1 #148200 on GenesisL1: 3D…
- PDB
- 6EZT
- Type
- protein
- Length
- 1,278 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-N-acetylglucosaminidase NAG2
- EC
- 3.2.1.52
- UniProt
- D9ISE0
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-N-acetylglucosaminidase NAG2 (EC 3.2.1.52) | protein | 639 | 28% helix, 26% strand | D9ISE0 |
Ligands and binding sites
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.81 | 0.96 | 41 | empty |
| 2 | 154 | 0.79 | 0.96 | 38 | empty |
| 3 | 436 | 0.77 | 0.86 | 69 | empty |
| 4 | 680 | 0.76 | 0.81 | 88 | empty |
| 5 | 127 | 0.73 | 0.93 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 2204 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6EZT · Crystal structure of GH20 Exo beta-N-Acetylglucosaminidase D437A inactive mutant from… · 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 D9ISE0
- Elsewhere: RCSB PDB 6EZT · PDBe 6EZT · UniProt D9ISE0
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