Research workbench
Crystal structure of the BIR2 ectodomain from arabidopsis thaliana.
Analyse Crystal structure of the BIR2 ectodomain from arabidopsis thaliana. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FG7
- Type
- protein
- Length
- 385 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inactive lrr receptor-like SERINE/THREONINE-protein kinase BIR2
- UniProt
- Q9LSI9
- Ligands
- NAG, FUC
- Pockets
- 6 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inactive lrr receptor-like SERINE/THREONINE-protein kinase BIR2 | protein | 193 | 22% helix, 21% strand | Q9LSI9 |
| B | Inactive lrr receptor-like SERINE/THREONINE-protein kinase BIR2 | protein | 192 | 21% helix, 21% strand | Q9LSI9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · chains A
- MLI · Malonate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.55 | 0.78 | 31 | empty |
| 2 | 160 | 0.47 | 0.77 | 33 | empty |
| 3 | 129 | 0.45 | 0.77 | 16 | empty |
| 4 | 89 | 0.35 | 0.75 | 17 | empty |
| 5 | 52 | 0.28 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 867 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6FG7 · Crystal structure of the BIR2 ectodomain from Arabidopsis thaliana. · the same entry in another collection · chain A against A, TM-score 1.00
- Q9LSI9 · AlphaFold monomer V2.0 prediction for inactive lrr receptor-like SERINE/THREONINE-protein… · a predicted model of the same protein · chain B 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 Q9LSI9
- Elsewhere: RCSB PDB 6FG7 · PDBe 6FG7 · UniProt Q9LSI9
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