MolNFT v1 · #40800 · protein
Bacteroides thetaiotaomicron GH84 O-glcnacase in complex with a imidazole-pugnac hybrid inhibitor
2J47 · Glucosaminidase: “Bacteroides thetaiotaomicron GH84 O-glcnacase in complex with a imidazole-pugnac hybrid inhibitor”. X-ray diffraction, 1 ligand (GDV), 10 pockets (best druggability 0.55). MolNFT v1 #40800 on GenesisL1: 3D…
- PDB
- 2J47
- Type
- protein
- Length
- 572 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosaminidase
- EC
- 3.2.1.52
- UniProt
- Q89ZI2
- Ligands
- GDV
- Pockets
- 10 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosaminidase (EC 3.2.1.52) | protein | 572 | 47% helix, 14% strand | Q89ZI2 |
Ligands and binding sites
- GDV · (5R,6R,7R,8S)-8-(acetylamino)-6,7-dihydroxy-5-(hydroxymethyl)-N-phenyl-1,5,6,7,8,8A-hexahydroimidazo[1,2-a]pyridine-2-carboxamide · ligand · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.55 | 0.84 | 21 | GDV, GOL |
| 2 | 110 | 0.43 | 0.77 | 17 | empty |
| 3 | 59 | 0.35 | 0.78 | 15 | empty |
| 4 | 55 | 0.34 | 0.77 | 11 | empty |
| 5 | 54 | 0.32 | 0.77 | 15 | empty |
Compared structures
- 2J47 · Bacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with a imidazole-pugnac hybrid… · 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 2J47 · PDBe 2J47 · UniProt Q89ZI2
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