MolNFT v1 · #126055 · protein
Crystal structure of glycogen phosphorylase B in complex with KS389
5LRF · Glycogen phosphorylase, muscle form: “Crystal structure of glycogen phosphorylase B in complex with KS389”. X-ray diffraction, 2 ligands (KS3, PLP), 13 pockets (best druggability 0.85). MolNFT v1 #126055 on GenesisL1: 3D structure…
- PDB
- 5LRF
- 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
- KS3, PLP
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 810 | 53% helix, 15% strand | P00489 |
Ligands and binding sites
- KS3 · (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(3-naphthalen-2-yl-1~{H}-1,2,4-triazol-5-yl)oxane-3,4,5-triol · ligand · 2 copies · chains A
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.85 | 0.95 | 59 | KS3, PLP |
| 2 | 93 | 0.71 | 0.94 | 29 | empty |
| 3 | 302 | 0.69 | 0.83 | 42 | empty |
| 4 | 108 | 0.50 | 0.81 | 18 | empty |
| 5 | 191 | 0.50 | 0.77 | 20 | DMS |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5LRF · Crystal structure of Glycogen Phosphorylase b in complex with KS389 · 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 5LRF · PDBe 5LRF · UniProt P00489
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