MolNFT v1 · #16089 · protein
Complex of glycogen phosphorylase with a transition state analogue nojirimycin tetrazole and phosphate in the T state
1NOK: “Complex of glycogen phosphorylase with a transition state analogue nojirimycin tetrazole and phosphate in the…”. X-ray diffraction, 2 ligands (PLP, NTZ), 14 pockets (best druggability 0.85). MolNFT v1 #16089 on GenesisL1: 3D…
- PDB
- 1NOK
- Type
- protein
- Length
- 831 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen phosphorylase
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- PLP, NTZ
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase (EC 2.4.1.1) | protein | 831 | 51% helix, 15% strand | P00489 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.85 | 0.96 | 52 | PLP, NTZ |
| 2 | 148 | 0.80 | 0.96 | 41 | empty |
| 3 | 300 | 0.70 | 0.84 | 35 | empty |
| 4 | 241 | 0.56 | 0.78 | 28 | empty |
| 5 | 118 | 0.53 | 0.82 | 19 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1NOK · Complex of glycogen phosphorylase with a transition state analogue nojirimycin tetrazole… · 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 1NOK · PDBe 1NOK · UniProt P00489
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