Research workbench
RAVER1 in complex with metavinculin L954 deletion mutant
Analyse RAVER1 in complex with metavinculin L954 deletion mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VF0
- Type
- protein
- Length
- 461 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vinculin; Ribonucleoprotein ptb-binding 1
- UniProt
- P18206, Q8IY67
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vinculin | protein | 178 | 70% helix, 2% strand | P18206 |
| B | Ribonucleoprotein ptb-binding 1 | protein | 283 | 34% helix, 29% strand | Q8IY67 |
Ligands and binding sites
- GOL · Glycerol · additive · 13 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.62 | 0.83 | 24 | GOL |
| 2 | 116 | 0.54 | 0.83 | 21 | GOL |
| 3 | 110 | 0.46 | 0.79 | 20 | GOL |
Interfaces
1 interface between chains.
- A–B · 799 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3VF0 · Raver1 in complex with metavinculin L954 deletion mutant · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IY67 · AlphaFold monomer V2.0 prediction for ribonucleoprotein ptb-binding 1 (Q8IY67) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P18206 · AlphaFold monomer V2.0 prediction for vinculin (P18206) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P18206
- Every structure of UniProt Q8IY67
- Elsewhere: RCSB PDB 3VF0 · PDBe 3VF0 · UniProt P18206 · UniProt Q8IY67
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