MolNFT v1 · #154199 · protein
Crystal structure of GH20 exo beta-N-acetylglucosaminidase from vibrio harveyi in complex with nag-thiazoline
6K35 · Beta-N-acetylglucosaminidase NAG2: “Crystal structure of GH20 exo beta-N-acetylglucosaminidase from vibrio harveyi in complex with nag-thiazoline”. X-ray diffraction, 1 ligand (NGT), 10 pockets (best druggability 0.67). MolNFT v1…
- PDB
- 6K35
- Type
- protein
- Length
- 1,280 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
- Ligands
- NGT
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-N-acetylglucosaminidase NAG2 (EC 3.2.1.52) | protein | 640 | 28% helix, 27% strand | D9ISE0 |
Ligands and binding sites
- NGT · 3ar,5r,6s,7r,7ar-5-hydroxymethyl-2-methyl-5,6,7,7A-tetrahydro-3AH-pyrano[3,2-d]thiazole-6,7-diol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.67 | 0.82 | 38 | NGT |
| 2 | 292 | 0.65 | 0.81 | 39 | NGT |
| 3 | 429 | 0.58 | 0.75 | 38 | empty |
| 4 | 67 | 0.46 | 0.83 | 15 | empty |
| 5 | 78 | 0.43 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 491 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6K35 · Crystal structure of GH20 exo beta-N-acetylglucosaminidase from Vibrio harveyi in complex… · 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 6K35 · PDBe 6K35 · UniProt D9ISE0
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