MolNFT v1 · #123852 · protein
Syngap coiled-coil trimer
5JXC · RAS/RAP GTPase-activating protein syngap: “Syngap coiled-coil trimer”. X-ray diffraction, 3 pockets (best druggability 0.59). MolNFT v1 #123852 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JXC
- Type
- protein
- Length
- 484 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS/RAP GTPase-activating protein syngap
- UniProt
- A0A0J9YUM2
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 5 distinct chains · 96% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS/RAP GTPase-activating protein syngap | protein | 86 | 97% helix, 0% strand | A0A0J9YUM2 |
| B | RAS/RAP GTPase-activating protein syngap | protein | 78 | 97% helix, 0% strand | A0A0J9YUM2 |
| C, D | RAS/RAP GTPase-activating protein syngap | protein | 78 | 97% helix, 0% strand | A0A0J9YUM2 |
| E | RAS/RAP GTPase-activating protein syngap | protein | 84 | 95% helix, 0% strand | A0A0J9YUM2 |
| F | RAS/RAP GTPase-activating protein syngap | protein | 80 | 94% helix, 0% strand | A0A0J9YUM2 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.59 | 0.90 | 14 | empty |
| 2 | 71 | 0.57 | 0.88 | 16 | empty |
| 3 | 58 | 0.35 | 0.78 | 14 | empty |
Interfaces
9 interfaces between chains.
- E–F · 1624 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1602 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1544 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 1509 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1499 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5JXC · SynGAP Coiled-coil trimer · 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 A0A0J9YUM2
- Elsewhere: RCSB PDB 5JXC · PDBe 5JXC · UniProt A0A0J9YUM2
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