Research workbench
Human RAVER1 RRM1 domain in complex with human vinculin tail domain vt
Analyse Human RAVER1 RRM1 domain in complex with human vinculin tail domain vt in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H2V
- Type
- protein
- Length
- 977 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vinculin; Raver-1
- UniProt
- B4DTM7, Q8IY67
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 64% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vinculin | protein | 174 | 71% helix, 2% strand | B4DTM7 |
| B | Vinculin | protein | 167 | 74% helix, 1% strand | B4DTM7 |
| C | Vinculin | protein | 167 | 74% helix, 1% strand | B4DTM7 |
| D | Vinculin | protein | 175 | 71% helix, 2% strand | B4DTM7 |
| E, G | Raver-1 | protein | 74 | 24% helix, 31% strand | Q8IY67 |
| F, H | Raver-1 | protein | 73 | 25% helix, 36% strand | Q8IY67 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.79 | 0.82 | 85 | empty |
| 2 | 740 | 0.74 | 0.80 | 60 | empty |
| 3 | 164 | 0.45 | 0.75 | 23 | empty |
| 4 | 167 | 0.45 | 0.75 | 24 | empty |
| 5 | 92 | 0.35 | 0.75 | 19 | empty |
Interfaces
10 interfaces between chains.
- B–F · 685 Ų buried · 14 hydrogen bonds · protein-protein
- C–G · 676 Ų buried · 13 hydrogen bonds · protein-protein
- D–H · 663 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 660 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 377 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3H2V · Human raver1 RRM1 domain in complex with human vinculin tail domain Vt · the same entry in another collection · chain H against H, TM-score 1.00
- Q8IY67 · AlphaFold monomer V2.0 prediction for ribonucleoprotein ptb-binding 1 (Q8IY67) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 B4DTM7
- Every structure of UniProt Q8IY67
- Elsewhere: RCSB PDB 3H2V · PDBe 3H2V · UniProt B4DTM7 · UniProt Q8IY67
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