MolNFT v1 · #5575 · protein
Human liver glycogen phosphorylase a complexed with glcnac and cp-526, 423
1EM6: “Human liver glycogen phosphorylase a complexed with glcnac and cp-526, 423”. X-ray diffraction, 3 ligands (NBG, PLP, CP4), 20 pockets (best druggability 0.86). MolNFT v1 #5575 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1EM6
- Type
- protein
- Length
- 1,574 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Liver glycogen phosphorylase
- EC
- 2.4.1.1
- UniProt
- P06737
- Ligands
- NBG, PLP, CP4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Liver glycogen phosphorylase (EC 2.4.1.1) | protein | 787 | 55% helix, 16% strand | P06737 |
Ligands and binding sites
- NBG · N-acetyl-beta-D-glucopyranosylamine · ligand · 2 copies · chains A, B
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- CP4 · Bis[5-chloro-1H-indol-2-yl-carbonyl-aminoethyl]-ethylene glycol · ligand · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · 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 | 1187 | 0.86 | 0.87 | 91 | CP4 |
| 2 | 266 | 0.84 | 0.96 | 50 | NBG, PLP |
| 3 | 263 | 0.84 | 0.96 | 51 | NBG, PLP |
| 4 | 67 | 0.70 | 0.96 | 25 | empty |
| 5 | 292 | 0.69 | 0.84 | 23 | MPD |
Interfaces
1 interface between chains.
- A–B · 2229 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1EM6 · Human liver glycogen phosphorylase a complexed with glcnac and cp-526,423 · 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 1EM6 · PDBe 1EM6 · UniProt P06737
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