Research workbench
Disproportionating enzyme 1 from arabidopsis - acarviostatin soak
Analyse Disproportionating enzyme 1 from arabidopsis - acarviostatin soak in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CSU
- Type
- protein
- Length
- 1,036 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
- AGL, HMC, GLC, BGC
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 4-alpha-glucanotransferase DPE1, CHLOROPLASTIC/AMYLOPLASTIC (EC 2.4.1.25) | protein | 518 | 46% helix, 12% strand | Q9LV91 |
Ligands and binding sites
- AGL · 4-amino-4,6-dideoxy-alpha-D-glucopyranose · ligand · 4 copies · chains A, B
- HMC · 5-hydroxymethyl-chonduritol · ligand · 4 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.76 | 0.81 | 76 | GLC, AGL, BGC, HMC |
| 2 | 694 | 0.76 | 0.81 | 74 | GLC, AGL, BGC, HMC |
| 3 | 329 | 0.76 | 0.87 | 36 | empty |
| 4 | 320 | 0.67 | 0.81 | 30 | empty |
| 5 | 309 | 0.64 | 0.80 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 2054 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5CSU · Disproportionating enzyme 1 from Arabidopsis - acarviostatin soak · the same entry in another collection · chain A against A, TM-score 1.00
- Q9LV91 · AlphaFold monomer V2.0 prediction for 4-alpha-glucanotransferase DPE1… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 5CSU · PDBe 5CSU · UniProt Q9LV91
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