Research workbench
Crystal structure of the SNX5 px domain in complex with the SEMA4C
Analyse Crystal structure of the SNX5 px domain in complex with the SEMA4C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N5Z
- Type
- protein
- Length
- 318 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sorting nexin-5,SEMAPHORIN-4C
- UniProt
- Q9Y5X3, Q9C0C4
- Ligands
- CL
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sorting nexin-5,SEMAPHORIN-4C | protein | 159 | 47% helix, 23% strand | Q9Y5X3, Q9C0C4 |
| B | Sorting nexin-5,SEMAPHORIN-4C | protein | 159 | 48% helix, 23% strand | Q9Y5X3, Q9C0C4 |
Ligands and binding sites
- CL · Chloride ion · ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.63 | 0.76 | 47 | empty |
| 2 | 310 | 0.55 | 0.75 | 45 | empty |
| 3 | 106 | 0.36 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1362 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6N5Z · Crystal structure of the SNX5 PX domain in complex with the Sema4C · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y5X3 · AlphaFold monomer V2.0 prediction for sorting nexin-5 (Q9Y5X3) · a predicted model of the same protein · chain A against A, TM-score 0.88
- Q9C0C4 · AlphaFold monomer V2.0 prediction for semaphorin-4C (Q9C0C4) · a predicted model of the same protein · chain B against A, TM-score 0.34
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 Q9Y5X3
- Every structure of UniProt Q9C0C4
- Elsewhere: RCSB PDB 6N5Z · PDBe 6N5Z · UniProt Q9Y5X3 · UniProt Q9C0C4
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