MolNFT v2 · #213427 · protein
6-BAP bound state of Arabidopsis AZG1
8IRN · Adenine/guanine permease AZG1: “6-BAP bound state of Arabidopsis AZG1”. Electron microscopy at 2.7, 2 ligands (EMU, NAG), 10 pockets (best druggability 0.77). MolNFT v2 #213427 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 8IRN
- Type
- protein
- Length
- 1,080 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Arabidopsis thaliana
- Molecule
- Adenine/guanine permease AZG1
- UniProt
- Q9SRK7
- Ligands
- EMU, NAG
- Pockets
- 10 · best druggability 0.77
Structure
electron microscopy · resolution 2.7 · 1 distinct chain · 60% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenine/guanine permease AZG1 | protein | 540 | 60% helix, 5% strand | Q9SRK7 |
Ligands and binding sites
- EMU · N-benzyl-9H-purin-6-amine · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1080 | 0.77 | 0.79 | 90 | empty |
| 2 | 1142 | 0.77 | 0.79 | 105 | empty |
| 3 | 771 | 0.75 | 0.80 | 67 | EMU |
| 4 | 743 | 0.74 | 0.79 | 64 | EMU |
| 5 | 204 | 0.65 | 0.83 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 3747 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- Q9SRK7 · AlphaFold monomer V2.0 prediction for ADENINE/GUANINE permease AZG1 (Q9SRK7) · a predicted model of the same protein · chain B against A, TM-score 0.78
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 Q9SRK7
- Elsewhere: RCSB PDB 8IRN · PDBe 8IRN · UniProt Q9SRK7
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