Research workbench
Human vinculin (residues 891-1066) in complex with pip
Analyse Human vinculin (residues 891-1066) in complex with pip in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PR9
- Type
- protein
- Length
- 1,033 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vinculin
- UniProt
- P18206
- Ligands
- PIO
- Pockets
- 10 · best druggability 0.53
Structure
x-ray diffraction · 5 distinct chains · 72% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vinculin | protein | 175 | 71% helix, 2% strand | P18206 |
| B, D | Vinculin | protein | 176 | 69% helix, 1% strand | P18206 |
| C | Vinculin | protein | 174 | 71% helix, 2% strand | P18206 |
| E | Vinculin | protein | 172 | 72% helix, 2% strand | P18206 |
| F | Vinculin | protein | 160 | 76% helix, 0% strand | P18206 |
Ligands and binding sites
- PIO · [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2, 3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate · ligand · 3 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.53 | 0.74 | 36 | empty |
| 2 | 170 | 0.52 | 0.79 | 24 | empty |
| 3 | 183 | 0.43 | 0.73 | 24 | empty |
| 4 | 139 | 0.41 | 0.75 | 17 | empty |
| 5 | 119 | 0.40 | 0.75 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 557 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 475 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 341 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 287 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 66 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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
- Elsewhere: RCSB PDB 4PR9 · PDBe 4PR9 · UniProt P18206
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