Research workbench
Crystal structure of zebrafish SNX25 px domain
Analyse Crystal structure of zebrafish SNX25 px domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XDZ
- Type
- protein
- Length
- 226 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellular trafficking protein
- UniProt
- C6K2H9
- Ligands
- NA, CL
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Cellular trafficking protein | protein | 113 | 40% helix, 27% strand | C6K2H9 |
| A | Cellular trafficking protein | protein | 113 | 46% helix, 27% strand | C6K2H9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.50 | 0.78 | 19 | empty |
| 2 | 58 | 0.39 | 0.80 | 15 | NA |
Interfaces
1 interface between chains.
- B–A · 718 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5XDZ · Crystal structure of zebrafish SNX25 PX domain · the same entry in another collection · chain B against B, 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 C6K2H9
- Elsewhere: RCSB PDB 5XDZ · PDBe 5XDZ · UniProt C6K2H9
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