MolNFT v1 · #126049 · protein
Structure of plastidial phosphorylase PHO1 from barley
5LR8 · Alpha-1,4 glucan phosphorylase: “Structure of plastidial phosphorylase PHO1 from barley”. X-ray diffraction, 1 ligand (PLP), 17 pockets (best druggability 0.83). MolNFT v1 #126049 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5LR8
- Type
- protein
- Length
- 1,687 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
- PLP
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1,4 glucan phosphorylase (EC 2.4.1.1) | protein | 844 | 54% helix, 14% strand | F2E0G2 |
| B | Alpha-1,4 glucan phosphorylase (EC 2.4.1.1) | protein | 843 | 53% helix, 15% strand | F2E0G2 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.83 | 0.84 | 101 | PLP, CIT |
| 2 | 1151 | 0.80 | 0.81 | 100 | empty |
| 3 | 936 | 0.79 | 0.81 | 80 | PLP |
| 4 | 150 | 0.78 | 0.95 | 40 | empty |
| 5 | 631 | 0.75 | 0.81 | 74 | empty |
Interfaces
1 interface between chains.
- A–B · 549 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5LR8 · Structure of plastidial phosphorylase Pho1 from Barley · 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 5LR8 · PDBe 5LR8 · UniProt F2E0G2
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