MolNFT v1 · #128927 · protein
Glycogen phosphorylase B in complex with 29B
5O56 · Glycogen phosphorylase, muscle form: “Glycogen phosphorylase B in complex with 29B”. X-ray diffraction, 2 ligands (PLP, 9L8), 11 pockets (best druggability 0.86). MolNFT v1 #128927 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5O56
- Type
- protein
- Length
- 810 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen phosphorylase, muscle form
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- PLP, 9L8
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 810 | 52% helix, 16% strand | P00489 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- 9L8 · (2~{R},3~{S},4~{R},5~{R},6~{R})-5-azanyl-2-(hydroxymethyl)-6-(3-naphthalen-2-yl-1~{H}-1,2,4-triazol-5-yl)oxane-3,4-diol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.86 | 0.96 | 50 | PLP, 9L8 |
| 2 | 126 | 0.78 | 0.96 | 36 | empty |
| 3 | 293 | 0.68 | 0.83 | 37 | empty |
| 4 | 104 | 0.52 | 0.82 | 20 | empty |
| 5 | 213 | 0.51 | 0.76 | 20 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5O56 · Glycogen Phosphorylase b in complex with 29b · 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 5O56 · PDBe 5O56 · UniProt P00489
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