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The structure of cellobiose phosphorylase from clostridium thermocellum in complex with phosphate
Analyse The structure of cellobiose phosphorylase from clostridium thermocellum in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QDE
- Type
- protein
- Length
- 1,622 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellobiose phosphorylase
- EC
- 2.4.1.20
- UniProt
- Q8VP44
- Ligands
- PO4
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cellobiose phosphorylase (EC 2.4.1.20) | protein | 811 | 30% helix, 28% strand | Q8VP44 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- 144 · Tris-hydroxymethyl-methyl-ammonium · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.84 | 0.85 | 121 | PO4, 144 |
| 2 | 173 | 0.82 | 0.97 | 28 | empty |
| 3 | 314 | 0.71 | 0.84 | 36 | empty |
| 4 | 338 | 0.71 | 0.84 | 35 | empty |
| 5 | 134 | 0.65 | 0.88 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 3739 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 3QDE · The structure of Cellobiose phosphorylase from Clostridium thermocellum in complex with… · 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 Q8VP44
- Elsewhere: RCSB PDB 3QDE · PDBe 3QDE · UniProt Q8VP44
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