Research workbench

Structure of vinculin VD1 / IPAA560-633 complex

Analyse Structure of vinculin VD1 / IPAA560-633 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GDC
Type: protein
Length: 259 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vinculin; Invasin ipaa
UniProt: P12003, P18010
Pockets: 2 · best druggability 0.33

Structure

x-ray diffraction · 2 distinct chains · 83% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vinculin	protein	238	83% helix, 0% strand	P12003
B	Invasin ipaa	protein	21	81% helix, 0% strand	P18010

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	65	0.33	0.76	12	empty
2	57	0.26	0.73	17	empty

Interfaces

1 interface between chains.

A–B · 1055 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2GDC · Structure of Vinculin VD1 / IpaA560-633 complex · 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 0.93
P18010 · AlphaFold monomer V2.0 prediction for invasin ipaa (P18010) · a predicted model of the same protein · chain B against A, TM-score 0.68

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
Every structure of UniProt P18010
Elsewhere: RCSB PDB 2GDC · PDBe 2GDC · UniProt P12003 · UniProt P18010

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