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Crystal structure of thermophilic dextranase from thermoanaerobacter pseudethanolicus, D312G mutant in complex with isomaltohexaose
Analyse Crystal structure of thermophilic dextranase from thermoanaerobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AXH
- Type
- protein
- Length
- 1,173 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dextranase
- EC
- 3.2.1.11
- UniProt
- B0KBZ7
- Ligands
- GLC, BGC, PO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dextranase (EC 3.2.1.11) | protein | 586 | 22% helix, 35% strand | B0KBZ7 |
| B | Dextranase (EC 3.2.1.11) | protein | 587 | 22% helix, 35% strand | B0KBZ7 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 9 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · chains B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1096 | 0.78 | 0.80 | 85 | empty |
| 2 | 154 | 0.65 | 0.86 | 31 | GLC |
| 3 | 341 | 0.64 | 0.80 | 56 | empty |
| 4 | 216 | 0.62 | 0.81 | 29 | GLC |
| 5 | 353 | 0.61 | 0.77 | 44 | empty |
Interfaces
1 interface between chains.
- A–B · 1196 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5AXH · Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus… · the same entry in another collection · 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 B0KBZ7
- Elsewhere: RCSB PDB 5AXH · PDBe 5AXH · UniProt B0KBZ7
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