MolNFT v1 · #136461 · protein
Crystal structure of burkholderia cenocepacia family 3 glycoside hydrolase (nagz) bound to pugnac
5UTQ · Beta-hexosaminidase: “Crystal structure of burkholderia cenocepacia family 3 glycoside hydrolase (nagz) bound to pugnac”. X-ray diffraction, 1 ligand (OAN), 5 pockets (best druggability 0.81). MolNFT v1 #136461 on GenesisL1: 3D…
- PDB
- 5UTQ
- Type
- protein
- Length
- 669 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-hexosaminidase
- EC
- 3.2.1.52
- UniProt
- A0A125HFC0
- Ligands
- OAN
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-hexosaminidase (EC 3.2.1.52) | protein | 334 | 46% helix, 12% strand | A0A125HFC0 |
| B | Beta-hexosaminidase (EC 3.2.1.52) | protein | 335 | 46% helix, 14% strand | A0A125HFC0 |
Ligands and binding sites
- OAN · O-(2-acetamido-2-deoxy D-glucopyranosylidene) amino-N-phenylcarbamate · ligand · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.81 | 0.85 | 91 | empty |
| 2 | 191 | 0.52 | 0.77 | 26 | OAN, MES |
| 3 | 160 | 0.50 | 0.78 | 24 | OAN |
| 4 | 51 | 0.26 | 0.73 | 14 | empty |
| 5 | 55 | 0.25 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1574 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5UTQ · 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 A0A125HFC0
- Elsewhere: RCSB PDB 5UTQ · PDBe 5UTQ · UniProt A0A125HFC0
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