Research workbench
Crystal structure of the BIR3 - SERK2 complex from arabidopsis thaliana.
Analyse Crystal structure of the BIR3 - SERK2 complex 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
- 6G3W
- Type
- protein
- Length
- 746 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Somatic embryogenesis receptor kinase 2; Probable inactive receptor kinase AT1G27190
- EC
- 2.7.11.1
- UniProt
- Q9XIC7, O04567
- Ligands
- NAG, BMA
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Somatic embryogenesis receptor kinase 2 (EC 2.7.11.1) | protein | 185 | 22% helix, 25% strand | Q9XIC7 |
| B | Probable inactive receptor kinase AT1G27190 | protein | 189 | 22% helix, 17% strand | O04567 |
| C | Somatic embryogenesis receptor kinase 2 (EC 2.7.11.1) | protein | 184 | 22% helix, 25% strand | Q9XIC7 |
| D | Probable inactive receptor kinase AT1G27190 | protein | 188 | 19% helix, 16% strand | O04567 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 2 copies
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, A, C
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 353 | 0.60 | 0.77 | 51 | EDO |
| 2 | 123 | 0.39 | 0.74 | 23 | empty |
| 3 | 93 | 0.36 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–D · 795 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 722 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 547 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6G3W · Crystal structure of the BIR3 - SERK2 complex from Arabidopsis thaliana. · the same entry in another collection · chain D against D, TM-score 1.00
- Q9XIC7 · AlphaFold monomer V2.0 prediction for somatic embryogenesis receptor kinase 2 (Q9XIC7) · a predicted model of the same protein · chain A against A, TM-score 0.99
- O04567 · AlphaFold monomer V2.0 prediction for probable inactive receptor kinase AT1G27190 (O04567) · 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 Q9XIC7
- Every structure of UniProt O04567
- Elsewhere: RCSB PDB 6G3W · PDBe 6G3W · UniProt Q9XIC7 · UniProt O04567
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