Research workbench
Crystal structure of human glycogen branching enzyme (GBE1) in complex with acarbose
Analyse Crystal structure of human glycogen branching enzyme (GBE1) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CLT
- Type
- protein
- Length
- 1,920 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1,4-alpha-glucan-branching enzyme
- EC
- 2.4.1.18
- UniProt
- Q04446
- Ligands
- AC1, GLC
- Pockets
- 15 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1,4-alpha-glucan-branching enzyme (EC 2.4.1.18) | protein | 646 | 31% helix, 24% strand | Q04446 |
| B | 1,4-alpha-glucan-branching enzyme (EC 2.4.1.18) | protein | 637 | 30% helix, 25% strand | Q04446 |
| C | 1,4-alpha-glucan-branching enzyme (EC 2.4.1.18) | protein | 637 | 30% helix, 24% strand | Q04446 |
Ligands and binding sites
- AC1 · 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose · ligand · 3 copies · chains A, B, C
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.61 | 0.75 | 45 | empty |
| 2 | 191 | 0.57 | 0.80 | 25 | empty |
| 3 | 166 | 0.56 | 0.81 | 30 | empty |
| 4 | 175 | 0.55 | 0.80 | 26 | empty |
| 5 | 195 | 0.51 | 0.77 | 38 | empty |
Interfaces
1 interface between chains.
- B–C · 291 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5CLT · Crystal structure of human glycogen branching enzyme (GBE1) in complex with acarbose · the same entry in another collection · chain A against A, TM-score 1.00
- Q04446 · AlphaFold monomer V2.0 prediction for 1,4-alpha-glucan-branching enzyme (Q04446) · a predicted model of the same protein · chain C 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 Q04446
- Elsewhere: RCSB PDB 5CLT · PDBe 5CLT · UniProt Q04446
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