Research workbench
Human vinculin head domain (VH1, residues 1-258) in complex with the vinculin binding site of the surface cell antigen 4 (SCA4-vbs-N; residues 412-434) from rickettsia rickettsii
Analyse Human vinculin head domain (VH1, residues 1-258) in complex with the vinculin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TJ5
- Type
- protein
- Length
- 281 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vinculin; Antigenic heat-stable 120 kda protein
- UniProt
- P18206, B0BXR4
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 81% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vinculin | protein | 254 | 81% helix, 1% strand | P18206 |
| B | Antigenic heat-stable 120 kda protein | protein | 27 | 78% helix, 0% strand | B0BXR4 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.49 | 0.82 | 18 | empty |
| 2 | 120 | 0.41 | 0.76 | 21 | empty |
| 3 | 85 | 0.40 | 0.77 | 13 | empty |
| 4 | 57 | 0.33 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1233 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3TJ5 · human vinculin head domain (Vh1, residues 1-258) in complex with the vinculin binding… · the same entry in another collection · chain A against A, TM-score 1.00
- P18206 · AlphaFold monomer V2.0 prediction for vinculin (P18206) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 B0BXR4
- Elsewhere: RCSB PDB 3TJ5 · PDBe 3TJ5 · UniProt P18206 · UniProt B0BXR4
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