MolNFT v1 · #115751 · protein
Disproportionating enzyme 1 from arabidopsis - acarbose soak
5CSY · 4-alpha-glucanotransferase DPE1, CHLOROPLASTIC/AMYLOPLASTIC: “Disproportionating enzyme 1 from arabidopsis - acarbose soak”. X-ray diffraction, 3 ligands (AC1, GLC, BGC), 9 pockets (best druggability 0.79). MolNFT v1 #115751 on…
- PDB
- 5CSY
- Type
- protein
- Length
- 1,023 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-alpha-glucanotransferase DPE1, CHLOROPLASTIC/AMYLOPLASTIC
- EC
- 2.4.1.25
- UniProt
- Q9LV91
- Ligands
- AC1, GLC, BGC
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-alpha-glucanotransferase DPE1, CHLOROPLASTIC/AMYLOPLASTIC (EC 2.4.1.25) | protein | 506 | 47% helix, 10% strand | Q9LV91 |
| B | 4-alpha-glucanotransferase DPE1, CHLOROPLASTIC/AMYLOPLASTIC (EC 2.4.1.25) | protein | 517 | 46% helix, 11% strand | Q9LV91 |
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 · chains B
- GLC · alpha-D-glucopyranose · sugar · 10 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.79 | 0.81 | 110 | GLC, AC1, EDO |
| 2 | 295 | 0.76 | 0.88 | 31 | empty |
| 3 | 492 | 0.75 | 0.83 | 56 | BGC, GLC |
| 4 | 51 | 0.69 | 0.98 | 25 | EDO |
| 5 | 273 | 0.63 | 0.80 | 28 | EDO |
Interfaces
1 interface between chains.
- A–B · 1946 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 glycan (glycosylation).
Compared structures
- Q9LV91 · AlphaFold monomer V2.0 prediction for 4-alpha-glucanotransferase DPE1… · 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 Q9LV91
- Elsewhere: RCSB PDB 5CSY · PDBe 5CSY · UniProt Q9LV91
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