MolNFT v1 · #150295 · protein
Refined crystal structure of the phosphorylase-heptulose 2-phosphate- oligosaccharide-AMP complex
6GPB · Glycogen phosphorylase B: “Refined crystal structure of the phosphorylase-heptulose 2-phosphate- oligosaccharide-AMP complex”. X-ray diffraction, 4 ligands (AMP, H2P, PLP), 14 pockets (best druggability 0.83). MolNFT v1 #150295 on…
- PDB
- 6GPB
- Type
- protein
- Length
- 828 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen phosphorylase B
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- AMP, H2P, PLP, GLC
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase B (EC 2.4.1.1) | protein | 828 | 53% helix, 15% strand | P00489 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A
- H2P · 1-deoxy-2-O-phosphono-alpha-D-gluco-hept-2-ulopyranose · ligand · chains A
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.83 | 0.95 | 45 | H2P, PLP |
| 2 | 287 | 0.72 | 0.86 | 63 | empty |
| 3 | 266 | 0.69 | 0.85 | 31 | empty |
| 4 | 158 | 0.56 | 0.81 | 30 | empty |
| 5 | 196 | 0.50 | 0.76 | 20 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 6GPB · Refined crystal structure of the phosphorylase-heptulose 2-phosphate-oligosaccharide-AMP… · 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 P00489
- Elsewhere: RCSB PDB 6GPB · PDBe 6GPB · UniProt P00489
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