Research workbench
Bacteroides thetaiotaomicron hexosaminidase with O- glcnacase activity
Analyse Bacteroides thetaiotaomicron hexosaminidase with O- glcnacase activity in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CHO
- Type
- protein
- Length
- 1,306 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosaminidase
- EC
- 3.2.1.52
- UniProt
- Q89ZI2
- Ligands
- CA
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosaminidase (EC 3.2.1.52) | protein | 641 | 42% helix, 19% strand | Q89ZI2 |
| B | Glucosaminidase (EC 3.2.1.52) | protein | 639 | 42% helix, 18% strand | Q89ZI2 |
| C, D | Glucosaminidase (EC 3.2.1.52) | protein | 13 | 0% helix, 31% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.68 | 0.78 | 48 | empty |
| 2 | 418 | 0.63 | 0.77 | 57 | empty |
| 3 | 317 | 0.61 | 0.78 | 40 | empty |
| 4 | 242 | 0.56 | 0.78 | 27 | empty |
| 5 | 71 | 0.55 | 0.86 | 19 | ACT, GOL |
Interfaces
3 interfaces between chains.
- A–B · 1039 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 410 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 410 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2CHO · Bacteroides thetaiotaomicron hexosaminidase with O-GlcNAcase activity · the same entry in another collection · chain A against A, TM-score 1.00
- Q89ZI2 · AlphaFold monomer V2.0 prediction for O-glcnacase BT_4395 (Q89ZI2) · a predicted model of the same protein · 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 Q89ZI2
- Elsewhere: RCSB PDB 2CHO · PDBe 2CHO · UniProt Q89ZI2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.