MolNFT v1 · #150228 · protein
Catalytic domain of starch synthase IV from arabidopsis thaliana bound to ADP and acarbose
6GNE · Probable starch synthase 4, CHLOROPLASTIC/AMYLOPLASTIC: “Catalytic domain of starch synthase IV from arabidopsis thaliana bound to ADP and acarbose”. X-ray diffraction, 3 ligands (AC1, ADP, GLC), 7 pockets (best druggability 0.82).…
- PDB
- 6GNE
- Type
- protein
- Length
- 987 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable starch synthase 4, CHLOROPLASTIC/AMYLOPLASTIC
- EC
- 2.4.1.21
- UniProt
- Q0WVX5
- Ligands
- AC1, ADP, GLC
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable starch synthase 4, CHLOROPLASTIC/AMYLOPLASTIC (EC 2.4.1.21) | protein | 493 | 41% helix, 22% strand | Q0WVX5 |
| B | Probable starch synthase 4, CHLOROPLASTIC/AMYLOPLASTIC (EC 2.4.1.21) | protein | 494 | 40% helix, 20% strand | Q0WVX5 |
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 · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.82 | 0.86 | 75 | GLC, AC1, ADP |
| 2 | 656 | 0.80 | 0.84 | 78 | GLC, AC1, ADP |
| 3 | 119 | 0.51 | 0.81 | 18 | empty |
| 4 | 126 | 0.44 | 0.76 | 20 | empty |
| 5 | 105 | 0.42 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 634 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6GNE · Catalytic domain of Starch Synthase IV from Arabidopsis thaliana bound to ADP and acarbose · the same entry in another collection · chain A against A, TM-score 1.00
- Q0WVX5 · AlphaFold monomer V2.0 prediction for probable starch synthase 4… · a predicted model of the same protein · chain A 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 Q0WVX5
- Elsewhere: RCSB PDB 6GNE · PDBe 6GNE · UniProt Q0WVX5
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