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Crystal structure of the vinculin tail and a pathway for activation

Analyse Crystal structure of the vinculin tail and a pathway for activation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1QKR
Type: protein
Length: 361 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vinculin
UniProt: P12003
Ligands: SO4
Pockets: 5 · best druggability 0.57

Structure

x-ray diffraction · 2 distinct chains · 72% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vinculin	protein	181	72% helix, 1% strand	P12003
B	Vinculin	protein	180	71% helix, 1% strand	P12003

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	112	0.57	0.85	26	empty
2	241	0.49	0.75	34	empty
3	95	0.39	0.77	17	empty
4	75	0.35	0.76	15	empty
5	60	0.29	0.74	14	empty

Interfaces

1 interface between chains.

A–B · 776 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 modified (engineered).

Compared structures

1QKR · Crystal structure of the vinculin tail and a pathway for activation · the same entry in another collection · chain A against A, TM-score 1.00
P12003 · AlphaFold monomer V2.0 prediction for vinculin (P12003) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 1QKR · PDBe 1QKR · UniProt P12003

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