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Crystal structure of thermophilic dextranase from thermoanaerobacter pseudethanolicus
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
- 5AXG
- Type
- protein
- Length
- 1,167 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
- K, PO4
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dextranase (EC 3.2.1.11) | protein | 583 | 22% helix, 36% strand | B0KBZ7 |
| B | Dextranase (EC 3.2.1.11) | protein | 584 | 23% helix, 36% strand | B0KBZ7 |
Ligands and binding sites
- K · Potassium ion · metal · chains B
- PO4 · Phosphate ion · ion · 8 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
- CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.77 | 0.79 | 86 | EDO |
| 2 | 492 | 0.73 | 0.82 | 65 | EDO |
| 3 | 198 | 0.61 | 0.82 | 26 | EDO |
| 4 | 250 | 0.59 | 0.79 | 31 | empty |
| 5 | 284 | 0.53 | 0.75 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 1136 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5AXG · 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 5AXG · PDBe 5AXG · UniProt B0KBZ7
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