MolNFT v1 · #126051 · protein
Plastidial phosphorylase from barley in complex with acarbose
5LRB · Alpha-1,4 glucan phosphorylase: “Plastidial phosphorylase from barley in complex with acarbose”. X-ray diffraction, 3 ligands (AC1, PLP, GLC), 19 pockets (best druggability 0.80). MolNFT v1 #126051 on GenesisL1: 3D structure…
- PDB
- 5LRB
- Type
- protein
- Length
- 1,686 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1,4 glucan phosphorylase
- EC
- 2.4.1.1
- UniProt
- F2E0G2
- Ligands
- AC1, PLP, GLC
- Pockets
- 19 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-1,4 glucan phosphorylase (EC 2.4.1.1) | protein | 843 | 53% helix, 15% strand | F2E0G2 |
Ligands and binding sites
- AC1 · 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.80 | 0.83 | 68 | GLC, PLP |
| 2 | 878 | 0.79 | 0.82 | 74 | GLC, PLP |
| 3 | 973 | 0.79 | 0.80 | 94 | empty |
| 4 | 653 | 0.75 | 0.81 | 71 | empty |
| 5 | 677 | 0.74 | 0.80 | 75 | empty |
Interfaces
1 interface between chains.
- A–B · 419 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5LRB · Plastidial phosphorylase from Barley in complex with acarbose · 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 F2E0G2
- Elsewhere: RCSB PDB 5LRB · PDBe 5LRB · UniProt F2E0G2
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