MolNFT v1 · #100278 · protein
Crystal structure of burkholderia cenocepacia family 3 glycoside hydrolase (nagz) bound to (3S,4R,5R,6S)-3-acetamido-4,5,6- trihydroxyazepane
4MSS · Beta-hexosaminidase 1: “Crystal structure of burkholderia cenocepacia family 3 glycoside hydrolase (nagz) bound to…”. X-ray diffraction, 1 ligand (2CZ), 4 pockets (best druggability 0.80). MolNFT v1 #100278 on GenesisL1: 3D…
- PDB
- 4MSS
- Type
- protein
- Length
- 678 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-hexosaminidase 1
- EC
- 3.2.1.52
- UniProt
- B4EA43
- Ligands
- 2CZ
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-hexosaminidase 1 (EC 3.2.1.52) | protein | 339 | 46% helix, 12% strand | B4EA43 |
Ligands and binding sites
- 2CZ · N-[(3S,4R,5R,6S)-4,5,6-trihydroxyazepan-3-yl]acetamide · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.80 | 0.86 | 86 | empty |
| 2 | 140 | 0.57 | 0.83 | 24 | 2CZ |
| 3 | 110 | 0.57 | 0.85 | 24 | 2CZ |
| 4 | 52 | 0.26 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1669 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 4MSS · Crystal structure of Burkholderia cenocepacia family 3 glycoside hydrolase (NagZ) bound… · 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 B4EA43
- Elsewhere: RCSB PDB 4MSS · PDBe 4MSS · UniProt B4EA43
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.