MolNFT v1 · #128721 · protein
Clostridium thermocellum cellodextrin phosphorylase with cellotetraose and phosphate bound
5NZ8: “Clostridium thermocellum cellodextrin phosphorylase with cellotetraose and phosphate bound”. X-ray diffraction, 2 ligands (BGC, PO4), 20 pockets (best druggability 0.88). MolNFT v1 #128721 on GenesisL1: 3D structure, binding sites…
- PDB
- 5NZ8
- Type
- protein
- Length
- 1,858 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellodextrin phosphorylase
- UniProt
- Q93HT8
- Ligands
- BGC, PO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellodextrin phosphorylase | protein | 884 | 31% helix, 26% strand | Q93HT8 |
| B | Cellodextrin phosphorylase | protein | 974 | 32% helix, 24% strand | Q93HT8 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 8 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.88 | 0.90 | 146 | empty |
| 2 | 386 | 0.74 | 0.84 | 45 | empty |
| 3 | 431 | 0.73 | 0.83 | 41 | empty |
| 4 | 99 | 0.73 | 0.94 | 26 | empty |
| 5 | 392 | 0.72 | 0.83 | 62 | empty |
Interfaces
1 interface between chains.
- A–B · 5071 Ų buried · 62 hydrogen bonds · protein-protein
Compared structures
- 5NZ8 · Clostridium thermocellum cellodextrin phosphorylase with cellotetraose and phosphate bound · 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 Q93HT8
- Elsewhere: RCSB PDB 5NZ8 · PDBe 5NZ8 · UniProt Q93HT8
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