Research workbench
Crystal structure of gpb in complex with sugar (N-[4-(5,6,7,8- tetrahydronaphthalen-2-YL)BUTANOYL]-beta-D-glucopyranosylamine)
Analyse Crystal structure of gpb in complex with sugar (N-[4-(5,6,7,8… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MI6
- Type
- protein
- Length
- 810 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
- 26V
- Pockets
- 12 · best druggability 0.83
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 | 810 | 53% helix, 15% strand | P00489 |
Ligands and binding sites
- 26V · N-[4-(5,6,7,8-tetrahydronaphthalen-2-yl)butanoyl]-beta-D-glucopyranosylamine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.83 | 0.95 | 43 | 26V |
| 2 | 139 | 0.79 | 0.96 | 39 | empty |
| 3 | 281 | 0.67 | 0.83 | 37 | empty |
| 4 | 105 | 0.53 | 0.83 | 20 | empty |
| 5 | 115 | 0.52 | 0.82 | 19 | empty |
Modifications
Observed in the structure: 1 modified (cofactor).
Compared structures
- 4MI6 · Crystal structure of Gpb in complex with SUGAR… · 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 4MI6 · PDBe 4MI6 · UniProt P00489
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