MolNFT v1 · #115503 · protein
Crystal structure of human glycogen branching enzyme (GBE1) in complex with acarbose
5CLT · 1,4-alpha-glucan-branching enzyme: “Crystal structure of human glycogen branching enzyme (GBE1) in complex with acarbose”. X-ray diffraction, 2 ligands (AC1, GLC), 15 pockets (best druggability 0.61). MolNFT v1 #115503 on GenesisL1…
- 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
- 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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