Research workbench
Crystal structure of afadin PDZ domain in complex with the C-terminal peptide from nectin-3
Analyse Crystal structure of afadin PDZ domain in complex with the C-terminal peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AXA
- Type
- protein
- Length
- 194 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Afadin, nectin-3
- UniProt
- Q9QZQ1, Q9JLB9
- Pockets
- 2 · best druggability 0.41
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Afadin, nectin-3 | protein | 97 | 14% helix, 38% strand | Q9QZQ1, Q9JLB9 |
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 | 152 | 0.41 | 0.74 | 25 | empty |
| 2 | 140 | 0.39 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 280 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3AXA · Crystal structure of afadin PDZ domain in complex with the C-terminal peptide from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9QZQ1 · AlphaFold monomer V2.0 prediction for afadin (Q9QZQ1) · a predicted model of the same protein · chain B against A, TM-score 0.86
- Q9JLB9 · AlphaFold monomer V2.0 prediction for nectin-3 (Q9JLB9) · a predicted model of the same protein · chain A against A, TM-score 0.28
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 Q9QZQ1
- Every structure of UniProt Q9JLB9
- Elsewhere: RCSB PDB 3AXA · PDBe 3AXA · UniProt Q9QZQ1 · UniProt Q9JLB9
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