Research workbench
Mdff model of the vinculin tail domain bound to F-actin
Analyse Mdff model of the vinculin tail domain bound to F-actin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JBI
- Type
- protein
- Length
- 865 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; Vinculin
- UniProt
- P68135, P12003
- Ligands
- ADP, MG
- Pockets
- 13 · best druggability 0.77
Structure
electron microscopy · 2 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Actin, alpha skeletal muscle | protein | 367 | 41% helix, 20% strand | P68135 |
| V | Vinculin | protein | 131 | 87% helix, 0% strand | P12003 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 115 | 0.77 | 0.96 | 26 | empty |
| 2 | 77 | 0.71 | 0.96 | 25 | empty |
| 3 | 52 | 0.70 | 0.97 | 21 | empty |
| 4 | 327 | 0.70 | 0.83 | 50 | ADP |
| 5 | 134 | 0.66 | 0.88 | 22 | ADP |
Interfaces
3 interfaces between chains.
- A–B · 1095 Ų buried · 16 hydrogen bonds · protein-protein
- B–V · 957 Ų buried · 5 hydrogen bonds · protein-protein
- A–V · 836 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3JBI · MDFF model of the vinculin tail domain bound to F-actin · the same entry in another collection · chain A against A, TM-score 1.00
- P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain A against A, TM-score 0.95
- P12003 · AlphaFold monomer V2.0 prediction for vinculin (P12003) · a predicted model of the same protein · chain V against A, TM-score 0.88
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 P68135
- Every structure of UniProt P12003
- Elsewhere: RCSB PDB 3JBI · PDBe 3JBI · UniProt P68135 · UniProt P12003
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