Research workbench
Human liver glycogen phosphorylase a complexed with riboflavin, N- acetyl-beta-D-glucopyranosylamine and cp-403,700
Analyse Human liver glycogen phosphorylase a complexed with riboflavin, N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L5R
- Type
- protein
- Length
- 1,581 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen phosphorylase, liver form
- EC
- 2.4.1.1
- UniProt
- P06737
- Ligands
- PLP, NBG, 700, RBF
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase, liver form (EC 2.4.1.1) | protein | 790 | 54% helix, 15% strand | P06737 |
| B | Glycogen phosphorylase, liver form (EC 2.4.1.1) | protein | 791 | 53% helix, 15% strand | P06737 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- NBG · N-acetyl-beta-D-glucopyranosylamine · ligand · chains A
- 700 · [5-chloro-1H-indol-2-carbonyl-phenylalaninyl]-azetidine-3-carboxylic acid · ligand · chains A, B
- RBF · Riboflavin · ligand · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.85 | 0.86 | 82 | 700 |
| 2 | 291 | 0.85 | 0.96 | 56 | PLP |
| 3 | 276 | 0.84 | 0.95 | 51 | NBG, PLP |
| 4 | 124 | 0.78 | 0.96 | 39 | empty |
| 5 | 313 | 0.69 | 0.83 | 24 | MRD |
Interfaces
1 interface between chains.
- A–B · 2379 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1L5R · Human liver glycogen phosphorylase a complexed with riboflavin… · the same entry in another collection · chain A against A, TM-score 1.00
- P06737 · AlphaFold monomer V2.0 prediction for glycogen phosphorylase, liver form (P06737) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P06737
- Elsewhere: RCSB PDB 1L5R · PDBe 1L5R · UniProt P06737
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