MolNFT v1 · #76289 · protein
Crystal structure of cellvibrio gilvus cellobiose phosphorylase complexed with phosphate and 1-deoxynojirimycin
3QG0: “Crystal structure of cellvibrio gilvus cellobiose phosphorylase complexed with phosphate and…”. X-ray diffraction, 3 ligands (NOJ, BGC, PO4), 13 pockets (best druggability 0.82). MolNFT v1 #76289 on GenesisL1: 3D structure, binding…
- PDB
- 3QG0
- Type
- protein
- Length
- 1,644 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellobiose phosphorylase
- EC
- 2.4.1.20
- UniProt
- O66264
- Ligands
- NOJ, BGC, PO4
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cellobiose phosphorylase (EC 2.4.1.20) | protein | 822 | 30% helix, 26% strand | O66264 |
Ligands and binding sites
- NOJ · 1-deoxynojirimycin · ligand · 2 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 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
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.82 | 0.83 | 123 | BGC, PO4, NOJ |
| 2 | 135 | 0.79 | 0.96 | 24 | empty |
| 3 | 229 | 0.72 | 0.87 | 36 | empty |
| 4 | 223 | 0.71 | 0.87 | 36 | empty |
| 5 | 268 | 0.69 | 0.84 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 3414 Ų buried · 61 hydrogen bonds · protein-protein
Compared structures
- 3QG0 · Crystal Structure of Cellvibrio gilvus Cellobiose Phosphorylase Complexed with Phosphate… · 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 O66264
- Elsewhere: RCSB PDB 3QG0 · PDBe 3QG0 · UniProt O66264
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