MolNFT v1 · #150230 · protein
Granule bound starch synthase I from cyanophora paradoxa bound to acarbose and ADP
6GNG · Granule-bound starch synthase: “Granule bound starch synthase I from cyanophora paradoxa bound to acarbose and ADP”. X-ray diffraction, 4 ligands (AC1, ADP, BGC), 8 pockets (best druggability 0.86). MolNFT v1 #150230 on GenesisL1…
- PDB
- 6GNG
- Type
- protein
- Length
- 1,051 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Granule-bound starch synthase
- UniProt
- A8V967
- Ligands
- AC1, ADP, BGC, GLC
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Granule-bound starch synthase | protein | 525 | 36% helix, 21% strand | A8V967 |
| B | Granule-bound starch synthase | protein | 526 | 36% helix, 21% strand | A8V967 |
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
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.86 | 0.87 | 99 | BGC, GLC, AC1, ADP |
| 2 | 1068 | 0.86 | 0.87 | 100 | BGC, GLC, AC1, ADP |
| 3 | 533 | 0.67 | 0.77 | 35 | empty |
| 4 | 450 | 0.57 | 0.74 | 46 | empty |
| 5 | 73 | 0.45 | 0.82 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 552 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6GNG · Granule Bound Starch Synthase I from Cyanophora paradoxa bound to acarbose and ADP · the same entry in another collection · chain A 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 A8V967
- Elsewhere: RCSB PDB 6GNG · PDBe 6GNG · UniProt A8V967
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