Research workbench
Crystal structure of the fyn-SH3 domain in complex with the high affinity peptide APP12
Analyse Crystal structure of the fyn-SH3 domain in complex with the high affinity… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZNX
- Type
- protein
- Length
- 266 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine-protein kinase fyn; APP12
- EC
- 2.7.10.2
- UniProt
- P06241
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 0% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine-protein kinase fyn (EC 2.7.10.2) | protein | 58 | 0% helix, 47% strand | P06241 |
| B, C | Tyrosine-protein kinase fyn (EC 2.7.10.2) | protein | 56 | 0% helix, 46% strand | P06241 |
| D | Tyrosine-protein kinase fyn (EC 2.7.10.2) | protein | 57 | 0% helix, 47% strand | P06241 |
| E, F, H | APP12 | protein | 10 | 0% helix, 0% strand | — |
| G | APP12 | protein | 9 | 0% helix, 0% strand | — |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.72 | 0.82 | 52 | empty |
| 2 | 70 | 0.37 | 0.77 | 15 | empty |
| 3 | 55 | 0.35 | 0.78 | 12 | empty |
| 4 | 59 | 0.32 | 0.76 | 13 | empty |
Interfaces
16 interfaces between chains.
- A–E · 498 Ų buried · 12 hydrogen bonds · protein-protein
- C–G · 497 Ų buried · 9 hydrogen bonds · protein-protein
- D–H · 487 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 485 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 406 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4ZNX · Crystal structure of the Fyn-SH3 domain in complex with the high affinity peptide APP12 · the same entry in another collection · chain H against H, TM-score 1.00
- P06241 · AlphaFold monomer V2.0 prediction for tyrosine-protein kinase fyn (P06241) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P06241
- Elsewhere: RCSB PDB 4ZNX · PDBe 4ZNX · UniProt P06241
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