MolNFT v2 · #151169 · protein
Granule Bound Starch Synthase from Cyanobacterium sp. CLg1 bound to acarbose and ADP
6GNF · Glycogen synthase: “Granule Bound Starch Synthase from Cyanobacterium sp. CLg1 bound to acarbose and ADP”. X-ray diffraction at 2.2, 5 ligands (ADP, GLC, BGC), 19 pockets (best druggability 0.86). MolNFT v2 #151169 on GenesisL1: 3D…
- PDB
- 6GNF
- Type
- protein
- Length
- 1,528 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Cyanobacterium sp. CLg1
- Molecule
- Glycogen synthase
- EC
- 2.4.1.21
- UniProt
- V5SNJ5
- Ligands
- ADP, GLC, BGC, AC1, SO4
- Pockets
- 19 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.2 · 3 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycogen synthase (EC 2.4.1.21) | protein | 522 | 39% helix, 20% strand | V5SNJ5 |
| B | Glycogen synthase (EC 2.4.1.21) | protein | 492 | 41% helix, 20% strand | V5SNJ5 |
| C | Glycogen synthase (EC 2.4.1.21) | protein | 514 | 40% helix, 19% strand | V5SNJ5 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A, C, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, C
- AC1 · 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose · sugar · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.86 | 0.87 | 116 | BGC, GLC, AC1, ADP, SO4 |
| 2 | 889 | 0.81 | 0.83 | 86 | BGC, GLC, AC1, ADP |
| 3 | 749 | 0.76 | 0.81 | 73 | ADP, GLC |
| 4 | 140 | 0.72 | 0.92 | 25 | empty |
| 5 | 257 | 0.59 | 0.79 | 30 | empty |
Interfaces
2 interfaces between chains.
- A–C · 853 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 498 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6GNF · Granule bound starch synthase from cyanobacterium sp. CLG1 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 V5SNJ5
- Elsewhere: RCSB PDB 6GNF · PDBe 6GNF · UniProt V5SNJ5
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