Research workbench
Vinculin head (1-258) in complex with a riam fragment
Analyse Vinculin head (1-258) in complex with a riam fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZDL
- Type
- protein
- Length
- 282 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vinculin; Amyloid beta A4 precursor protein-binding family B member 1-interacting protein
- UniProt
- P12003, Q7Z5R6
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 83% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vinculin | protein | 256 | 85% helix, 1% strand | P12003 |
| B | Amyloid beta A4 precursor protein-binding family B member 1-interacting protein | protein | 26 | 69% helix, 0% strand | Q7Z5R6 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.62 | 0.90 | 17 | empty |
| 2 | 141 | 0.44 | 0.75 | 18 | empty |
| 3 | 55 | 0.34 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1169 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3ZDL · Vinculin head (1-258) in complex with a RIAM fragment · the same entry in another collection · chain A against A, TM-score 1.00
- P12003 · AlphaFold monomer V2.0 prediction for vinculin (P12003) · a predicted model of the same protein · chain A against A, TM-score 0.89
- Q7Z5R6 · AlphaFold monomer V2.0 prediction for amyloid beta A4 precursor protein-binding family B… · a predicted model of the same protein · chain B against A, TM-score 0.71
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 P12003
- Every structure of UniProt Q7Z5R6
- Elsewhere: RCSB PDB 3ZDL · PDBe 3ZDL · UniProt P12003 · UniProt Q7Z5R6
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