Research workbench
S8-msrk-S8-SP11 complex
Analyse S8-msrk-S8-SP11 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KYW
- Type
- protein
- Length
- 867 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor protein kinase SRK8; S locus protein 11
- UniProt
- Q39276, Q9SE17
- Ligands
- NAG
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor protein kinase SRK8 | protein | 389 | 7% helix, 43% strand | Q39276 |
| B | Receptor protein kinase SRK8 | protein | 386 | 6% helix, 41% strand | Q39276 |
| C, D | S locus protein 11 | protein | 46 | 15% helix, 35% strand | Q9SE17 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 855 | 0.84 | 0.86 | 96 | empty |
| 2 | 797 | 0.83 | 0.86 | 98 | empty |
| 3 | 177 | 0.52 | 0.79 | 30 | empty |
| 4 | 198 | 0.50 | 0.77 | 28 | empty |
| 5 | 101 | 0.48 | 0.80 | 16 | empty |
Interfaces
6 interfaces between chains.
- B–C · 904 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 899 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 788 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 469 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 463 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6KYW · S8-mSRK-S8-SP11 complex · 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 Q39276
- Every structure of UniProt Q9SE17
- Elsewhere: RCSB PDB 6KYW · PDBe 6KYW · UniProt Q39276 · UniProt Q9SE17
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