Research workbench
Rerefinement of chicken vinculin
Analyse Rerefinement of chicken vinculin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NR7
- Type
- protein
- Length
- 1,086 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vinculin
- UniProt
- P12003
- Ligands
- KYG, SO4, PO4
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 70% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vinculin | protein | 1086 | 70% helix, 1% strand | P12003 |
Ligands and binding sites
- KYG · (1R,2R,3S,4R,5R,6S)-4-{[(S)-[(2S)-2,3-dihydroxypropoxy](hydroxy)phosphoryl]oxy}-3,5,6-trihydroxycyclohexane-1,2-diyl bis[dihydrogen (phosphate)] · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.83 | 0.88 | 64 | empty |
| 2 | 350 | 0.70 | 0.83 | 37 | empty |
| 3 | 372 | 0.70 | 0.82 | 47 | empty |
| 4 | 73 | 0.64 | 0.92 | 22 | empty |
| 5 | 206 | 0.57 | 0.80 | 34 | empty |
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 P12003
- Elsewhere: RCSB PDB 6NR7 · PDBe 6NR7 · UniProt P12003
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