MolNFT v1 · #148838 · protein
Crystal structure of the ANX1 ectodomain from arabidopsis thaliana
6FIG · Receptor-like protein kinase ANXUR1: “Crystal structure of the ANX1 ectodomain from arabidopsis thaliana”. X-ray diffraction, 3 ligands (NAG, FUC, CA), 4 pockets (best druggability 0.83). MolNFT v1 #148838 on GenesisL1: 3D…
- PDB
- 6FIG
- Type
- protein
- Length
- 771 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor-like protein kinase ANXUR1
- EC
- 2.7.11.1
- UniProt
- Q9SR05
- Ligands
- NAG, FUC, CA
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor-like protein kinase ANXUR1 (EC 2.7.11.1) | protein | 386 | 10% helix, 41% strand | Q9SR05 |
| B | Receptor-like protein kinase ANXUR1 (EC 2.7.11.1) | protein | 385 | 9% helix, 41% strand | Q9SR05 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · chains A
- CA · Calcium ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
- CIT · Citric acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.83 | 0.84 | 99 | EDO |
| 2 | 621 | 0.76 | 0.82 | 56 | empty |
| 3 | 310 | 0.66 | 0.81 | 50 | empty |
| 4 | 78 | 0.41 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 732 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan (N-glycosylation).
Compared structures
- 6FIG · Crystal structure of the ANX1 ectodomain from Arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00
- Q9SR05 · AlphaFold monomer V2.0 prediction for receptor-like protein kinase ANXUR1 (Q9SR05) · a predicted model of the same protein · chain B 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 Q9SR05
- Elsewhere: RCSB PDB 6FIG · PDBe 6FIG · UniProt Q9SR05
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