Research workbench
Bacteroides thetaiotaomicron GH84 O-glcnacase in complex with N-butyl-thiazoline inhibitor
Analyse Bacteroides thetaiotaomicron GH84 O-glcnacase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J4G
- Type
- protein
- Length
- 1,166 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hyaluronoglucosaminidase
- EC
- 3.2.1.52
- UniProt
- Q89ZI2
- Ligands
- NB1
- Pockets
- 16 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hyaluronoglucosaminidase (EC 3.2.1.52) | protein | 586 | 46% helix, 14% strand | Q89ZI2 |
| B | Hyaluronoglucosaminidase (EC 3.2.1.52) | protein | 580 | 45% helix, 15% strand | Q89ZI2 |
Ligands and binding sites
- NB1 · (3ar,5r,6s,7r,7ar)-5-(hydroxymethyl)-2-propyl-5,6,7,7A-tetrahydro-3AH-pyrano[3,2-d][1,3]thiazole-6,7-diol · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.60 | 0.86 | 24 | NB1, ACT, GOL |
| 2 | 111 | 0.58 | 0.85 | 25 | NB1, GOL |
| 3 | 147 | 0.43 | 0.75 | 24 | ACT |
| 4 | 117 | 0.42 | 0.77 | 19 | empty |
| 5 | 116 | 0.38 | 0.74 | 20 | empty |
Compared structures
- 2J4G · Bacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with n-butyl- thiazoline… · 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 B 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 2J4G · PDBe 2J4G · UniProt Q89ZI2
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