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: 2VZA
Type: protein
Length: 2,368 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cell filamentation protein
UniProt: Q6G2A9
Ligands: SO4
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Cell filamentation protein	protein	296	46% helix, 11% strand	Q6G2A9

Ligands and binding sites

SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	998	0.81	0.82	78	SO4
2	821	0.77	0.81	59	SO4
3	1084	0.77	0.79	85	SO4
4	1032	0.76	0.78	77	SO4
5	607	0.69	0.78	92	SO4

Interfaces

10 interfaces between chains.

E–G · 1137 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 1128 Å² buried · 13 hydrogen bonds · protein-protein
F–H · 1053 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 1022 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 628 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

2VZA · Type IV secretion system effector protein BepA · the same entry in another collection · chain H against H, 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 2VZA · PDBe 2VZA · UniProt Q6G2A9

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