Research workbench
Catalytic domain of starch synthase IV from arabidopsis thaliana bound to ADP and acarbose
Analyse Catalytic domain of starch synthase IV from arabidopsis thaliana bound to ADP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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