Research workbench
Glycogen phosphorylase complexed with 2,5-dihydroxy-3-(beta-D- glucopyranosyl)-chlorobenzene and 2,5-dihydroxy-4-(beta-D- glucopyranosyl)-chlorobenzene
Analyse Glycogen phosphorylase complexed with 2,5-dihydroxy-3-(beta-D… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NP7
- Type
- protein
- Length
- 813 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycogen phosphorylase, muscle form
- EC
- 2.4.1.1
- UniProt
- P00489
- Ligands
- Z15, Z16
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen phosphorylase, muscle form (EC 2.4.1.1) | protein | 813 | 53% helix, 15% strand | P00489 |
Ligands and binding sites
- Z15 · (1S)-1,5-anhydro-1-(4-chloro-2,5-dihydroxyphenyl)-D-glucitol · ligand · 2 copies · chains A
- Z16 · (1S)-1,5-anhydro-1-(3-chloro-2,5-dihydroxyphenyl)-D-glucitol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.79 | 0.96 | 33 | Z15, Z16 |
| 2 | 140 | 0.79 | 0.96 | 41 | empty |
| 3 | 449 | 0.70 | 0.81 | 52 | Z15 |
| 4 | 124 | 0.53 | 0.81 | 18 | empty |
| 5 | 114 | 0.52 | 0.81 | 24 | empty |
Modifications
Observed in the structure: 1 modified (cofactor).
Compared structures
- 3NP7 · Glycogen phosphorylase complexed with 2,5-dihydroxy-3-(beta-D-glucopyranosyl)-chlorobenzen… · 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 P00489
- Elsewhere: RCSB PDB 3NP7 · PDBe 3NP7 · UniProt P00489
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