MolNFT v1 · #111693 · protein
The crystal structure of a glycosyl hydrolase of GH3 family member from [mycobacterium smegmatis str. MC2 155
4YYF · Beta-N-acetylhexosaminidase: “The crystal structure of a glycosyl hydrolase of GH3 family member from [mycobacterium smegmatis str. MC2 155”. X-ray diffraction, 1 ligand (NA), 10 pockets (best druggability 0.80). MolNFT v1 #111693…
- PDB
- 4YYF
- Type
- protein
- Length
- 981 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-N-acetylhexosaminidase
- EC
- 3.2.1.52
- UniProt
- A0QPD6
- Ligands
- NA
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 331 | 44% helix, 12% strand | A0QPD6 |
| B | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 330 | 44% helix, 12% strand | A0QPD6 |
| C | Beta-N-acetylhexosaminidase (EC 3.2.1.52) | protein | 320 | 40% helix, 13% strand | A0QPD6 |
Ligands and binding sites
- NA · Sodium ion · metal · 3 copies · chains A, B
- ACT · Acetate ion · additive · 6 copies · chains A, B, C
- FMT · Formic acid · additive · chains A
- GOL · Glycerol · additive · chains 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.80 | 0.81 | 104 | ACT |
| 2 | 171 | 0.69 | 0.88 | 35 | empty |
| 3 | 320 | 0.66 | 0.81 | 35 | empty |
| 4 | 364 | 0.64 | 0.79 | 56 | empty |
| 5 | 138 | 0.57 | 0.83 | 26 | ACT |
Interfaces
3 interfaces between chains.
- B–C · 793 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 741 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 208 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 4YYF · The crystal structure of a glycosyl hydrolase of GH3 family member from [Mycobacterium… · 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 A0QPD6
- Elsewhere: RCSB PDB 4YYF · PDBe 4YYF · UniProt A0QPD6
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