Research workbench

Type IV secretion system effector protein bepa

Analyse Type IV secretion system effector protein bepa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VY3
Type: protein
Length: 582 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cell filamentation protein
UniProt: Q6G2A9
Ligands: NI, CL
Pockets: 9 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cell filamentation protein	protein	291	46% helix, 13% strand	Q6G2A9

Ligands and binding sites

NI · Nickel (II) ion · metal · 4 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	238	0.65	0.83	34	empty
2	303	0.65	0.81	35	empty
3	558	0.63	0.75	55	CL
4	579	0.63	0.75	46	CL
5	104	0.41	0.76	18	empty

Interfaces

1 interface between chains.

A–B · 639 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 modified (engineered).

Compared structures

2VY3 · Type IV secretion system effector protein BepA · the same entry in another collection · chain A against A, TM-score 1.00
Q6G2A9 · AlphaFold monomer V2.0 prediction for protein adenylyltransferase (Q6G2A9) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q6G2A9
Elsewhere: RCSB PDB 2VY3 · PDBe 2VY3 · UniProt Q6G2A9

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