MolNFT v1 · #126050 · protein
Plastidial phosphorylase phoi from barley in complex with maltotetraose
5LRA · Alpha-1,4 glucan phosphorylase: “Plastidial phosphorylase phoi from barley in complex with maltotetraose”. X-ray diffraction, 3 ligands (PLP, GLC, BGC), 18 pockets (best druggability 0.83). MolNFT v1 #126050 on GenesisL1: 3D…
- PDB
- 5LRA
- 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
- PLP, GLC, BGC
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 14% 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, 14% strand | F2E0G2 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 10 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.83 | 0.85 | 110 | BGC, GLC, PLP |
| 2 | 761 | 0.82 | 0.85 | 92 | BGC, GLC, PLP |
| 3 | 116 | 0.78 | 0.97 | 26 | empty |
| 4 | 848 | 0.78 | 0.81 | 68 | empty |
| 5 | 140 | 0.77 | 0.95 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 513 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5LRA · Plastidial phosphorylase PhoI from barley in complex with maltotetraose · 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 5LRA · PDBe 5LRA · UniProt F2E0G2
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