MolNFT v1 · #85717 · protein

Crystal structure of VIRB8 from brucella suis in complex with interaction inhibitor 2-(butylamino)-8-quinolinol

4AKY · Type IV secretion system protein VIRB8: “Crystal structure of VIRB8 from brucella suis in complex with interaction inhibitor…”. X-ray diffraction, 1 ligand (4LL), 8 pockets (best druggability 0.84). MolNFT v1 #85717 on GenesisL1: 3D…

PDB: 4AKY
Type: protein
Length: 670 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Type IV secretion system protein VIRB8
UniProt: Q7CEG3
Ligands: 4LL
Pockets: 8 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Type IV secretion system protein VIRB8	protein	134	40% helix, 37% strand	Q7CEG3

Ligands and binding sites

4LL · 2-(butylamino)quinolin-8-ol · ligand · 5 copies · chains A, B, C, D, E

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

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	253	0.84	0.96	33	empty
2	842	0.83	0.86	88	empty
3	1086	0.76	0.79	88	4LL
4	99	0.40	0.76	19	4LL
5	76	0.39	0.77	17	4LL

Interfaces

6 interfaces between chains.

A–C · 923 Å² buried · 7 hydrogen bonds · protein-protein
D–E · 897 Å² buried · 4 hydrogen bonds · protein-protein
C–E · 844 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 593 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 483 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4AKY · CRYSTAL STRUCTURE OF VIRB8 FROM BRUCELLA SUIS IN COMPLEX WITH INTERACTION INHIBITOR… · the same entry in another collection · chain A against A, TM-score 1.00
Q7CEG3 · AlphaFold monomer V2.0 prediction for type IV secretion system protein VIRB8 (Q7CEG3) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q7CEG3
Elsewhere: RCSB PDB 4AKY · PDBe 4AKY · UniProt Q7CEG3

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