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Structure of a vgrg vibrio cholerae toxin acd domain in complex with ADP and mn++

Analyse Structure of a vgrg vibrio cholerae toxin acd domain in complex with ADP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4E1D
Type: protein
Length: 356 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vgrg protein
UniProt: Q9KS45
Ligands: ADP, MN, SO4
Pockets: 1 · best druggability 0.62

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Vgrg protein	protein	356	35% helix, 25% strand	Q9KS45

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
MN · Manganese (II) ion · metal · 2 copies · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	354	0.62	0.78	42	ADP, MN, SO4

Compared structures

4E1D · Structure of a VgrG Vibrio cholerae toxin ACD domain in complex with ADP and Mn++ · the same entry in another collection · chain A against A, TM-score 1.00
Q9KS45 · AlphaFold monomer V2.0 prediction for actin cross-linking toxin VGRG1 (Q9KS45) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q9KS45
Elsewhere: RCSB PDB 4E1D · PDBe 4E1D · UniProt Q9KS45

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