Research workbench
Thermobaculum terrenum O-GlcNAc hydrolase mutant - D120N
Analyse Thermobaculum terrenum O-GlcNAc hydrolase mutant - D120N in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DIY
- Type
- protein
- Length
- 935 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.06
- Source
- Thermobaculum terrenum; SYNTHETIC CONSTRUCT
- Molecule
- TGF-beta-activated kinase 1 and MAP3K7-binding protein 1; Hyaluronidase
- UniProt
- Q15750, D1CDN2
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · resolution 2.06 · 3 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P, Q | TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 | protein | 5 | 0% helix, 0% strand | Q15750 |
| A | Hyaluronidase | protein | 463 | 53% helix, 11% strand | D1CDN2 |
| B | Hyaluronidase | protein | 462 | 53% helix, 10% strand | D1CDN2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains P, A, Q, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1018 | 0.78 | 0.80 | 90 | empty |
| 2 | 79 | 0.51 | 0.85 | 23 | empty |
| 3 | 119 | 0.43 | 0.76 | 20 | empty |
| 4 | 109 | 0.39 | 0.75 | 25 | empty |
| 5 | 71 | 0.38 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 985 Ų buried · 14 hydrogen bonds · protein-protein
- Q–B · 305 Ų buried · 2 hydrogen bonds · protein-protein
- P–A · 299 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (O-glycosylation).
Compared structures
- 5DIY · Thermobaculum terrenum O-glcnac hydrolase mutant - D120N · the same entry in another collection · chain A against A, TM-score 1.00
- Q15750 · AlphaFold monomer V2.0 prediction for TGF-beta-activated kinase 1 and MAP3K7-binding… · a predicted model of the same protein · chain P against A, TM-score 0.80
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 Q15750
- Every structure of UniProt D1CDN2
- Elsewhere: RCSB PDB 5DIY · PDBe 5DIY · UniProt Q15750 · UniProt D1CDN2
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