Research workbench
Cryo-EM reconstruction of the metavinculin-actin interface
Analyse Cryo-EM reconstruction of the metavinculin-actin interface in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JBK
- Type
- protein
- Length
- 865 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Actin, alpha skeletal muscle; Metavinculin
- UniProt
- P68135, P18206
- Ligands
- ADP, MG
- Pockets
- 12 · best druggability 0.74
Structure
electron microscopy · 2 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Actin, alpha skeletal muscle | protein | 367 | 38% helix, 20% strand | P68135 |
| M | Metavinculin | protein | 131 | 86% helix, 0% strand | P18206 |
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
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.74 | 0.95 | 28 | empty |
| 2 | 92 | 0.73 | 0.95 | 31 | empty |
| 3 | 238 | 0.67 | 0.84 | 35 | ADP |
| 4 | 370 | 0.66 | 0.80 | 51 | empty |
| 5 | 219 | 0.66 | 0.84 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1164 Ų buried · 16 hydrogen bonds · protein-protein
- B–M · 831 Ų buried · 2 hydrogen bonds · protein-protein
- A–M · 814 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3JBK · Cryo-EM reconstruction of the metavinculin-actin interface · 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
- P18206 · AlphaFold monomer V2.0 prediction for vinculin (P18206) · a predicted model of the same protein · chain M against A, TM-score 0.91
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 P18206
- Elsewhere: RCSB PDB 3JBK · PDBe 3JBK · UniProt P68135 · UniProt P18206
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