MolNFT v1 · #122409 · protein
Crystal structure of beta-N-acetylglucosaminidase-like protein from corynebacterium glutamicum
5IOB · Beta-glucosidase-related glycosidases: “Crystal structure of beta-N-acetylglucosaminidase-like protein from corynebacterium glutamicum”. X-ray diffraction, 2 ligands (SO4, CL), 20 pockets (best druggability 0.70). MolNFT v1 #122409…
- PDB
- 5IOB
- Type
- protein
- Length
- 2,523 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase-related glycosidases
- EC
- 3.2.1.52
- UniProt
- Q8NLT5
- Ligands
- SO4, CL
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 8 distinct chains · 46% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucosidase-related glycosidases (EC 3.2.1.52) | protein | 316 | 46% helix, 11% strand | Q8NLT5 |
| B | Beta-glucosidase-related glycosidases (EC 3.2.1.52) | protein | 313 | 47% helix, 12% strand | Q8NLT5 |
| C | Beta-glucosidase-related glycosidases (EC 3.2.1.52) | protein | 321 | 44% helix, 11% strand | Q8NLT5 |
| D | Beta-glucosidase-related glycosidases (EC 3.2.1.52) | protein | 316 | 47% helix, 11% strand | Q8NLT5 |
| E | Beta-glucosidase-related glycosidases (EC 3.2.1.52) | protein | 312 | 45% helix, 11% strand | Q8NLT5 |
| F | Beta-glucosidase-related glycosidases (EC 3.2.1.52) | protein | 313 | 48% helix, 12% strand | Q8NLT5 |
| G | Beta-glucosidase-related glycosidases (EC 3.2.1.52) | protein | 323 | 44% helix, 11% strand | Q8NLT5 |
| H | Beta-glucosidase-related glycosidases (EC 3.2.1.52) | protein | 309 | 48% helix, 12% strand | Q8NLT5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains C, G
- CL · Chloride ion · ion · chains G
- GOL · Glycerol · additive · 4 copies · chains A, C, D, E, G, H
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, C, D, E, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.70 | 0.78 | 57 | empty |
| 2 | 473 | 0.67 | 0.78 | 53 | empty |
| 3 | 115 | 0.55 | 0.83 | 29 | GOL |
| 4 | 292 | 0.53 | 0.75 | 40 | empty |
| 5 | 92 | 0.45 | 0.79 | 20 | GOL |
Interfaces
8 interfaces between chains.
- E–F · 960 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 959 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 956 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 953 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 448 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 64 modified (engineered).
Compared structures
- 5IOB · Crystal structure of beta-N-acetylglucosaminidase-like protein from Corynebacterium… · 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 Q8NLT5
- Elsewhere: RCSB PDB 5IOB · PDBe 5IOB · UniProt Q8NLT5
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