MolNFT v1 · #140103 · protein
Crystal structure of the complex between the vinculin D1 domain and alphae-catenin
5Y04: “Crystal structure of the complex between the vinculin D1 domain and alphae-catenin”. X-ray diffraction, 1 pocket (best druggability 0.58). MolNFT v1 #140103 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Y04
- Type
- protein
- Length
- 303 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vinculin; Catenin alpha-1
- UniProt
- Q64727, P26231
- Pockets
- 1 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vinculin | protein | 239 | 80% helix, 1% strand | Q64727 |
| B | Catenin alpha-1 | protein | 64 | 61% helix, 0% strand | P26231 |
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.58 | 0.78 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1884 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5Y04 · Crystal Structure of the complex between the vinculin D1 domain and alphaE-catenin · the same entry in another collection · chain A against A, TM-score 1.00
- Q64727 · AlphaFold monomer V2.0 prediction for vinculin (Q64727) · a predicted model of the same protein · chain A against A, TM-score 0.89
- P26231 · AlphaFold monomer V2.0 prediction for catenin alpha-1 (P26231) · a predicted model of the same protein · chain B against A, TM-score 0.53
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 Q64727
- Every structure of UniProt P26231
- Elsewhere: RCSB PDB 5Y04 · PDBe 5Y04 · UniProt Q64727 · UniProt P26231
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