Research workbench
Family 37 trehalase from escherichia COLI in complex with casuarine-6- O-alpha-glucopyranose
Analyse Family 37 trehalase from escherichia COLI in complex with casuarine-6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JJB
- Type
- protein
- Length
- 1,997 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic trehalase
- EC
- 3.2.1.28
- UniProt
- P13482
- Ligands
- 3CU, GLC, SO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic trehalase (EC 3.2.1.28) | protein | 504 | 51% helix, 9% strand | P13482 |
| B | Periplasmic trehalase (EC 3.2.1.28) | protein | 493 | 53% helix, 9% strand | P13482 |
| C | Periplasmic trehalase (EC 3.2.1.28) | protein | 500 | 52% helix, 9% strand | P13482 |
| D | Periplasmic trehalase (EC 3.2.1.28) | protein | 500 | 52% helix, 9% strand | P13482 |
Ligands and binding sites
- 3CU · Casuarine · ligand · 4 copies · chains A, B, C, D
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 38 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.85 | 0.92 | 55 | SO4 |
| 2 | 779 | 0.81 | 0.84 | 72 | SO4 |
| 3 | 250 | 0.79 | 0.91 | 41 | 3CU, GLC, SO4 |
| 4 | 858 | 0.73 | 0.78 | 84 | SO4 |
| 5 | 265 | 0.72 | 0.86 | 34 | 3CU, GLC, SO4 |
Interfaces
5 interfaces between chains.
- B–D · 2144 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 2110 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 347 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 154 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 64 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2JJB · Family 37 trehalase from Escherichia coli in complex with casuarine-6… · the same entry in another collection · chain D against D, TM-score 1.00
- P13482 · AlphaFold monomer V2.0 prediction for periplasmic trehalase (P13482) · 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 P13482
- Elsewhere: RCSB PDB 2JJB · PDBe 2JJB · UniProt P13482
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.