MolNFT v1 · #85718 · protein

Crystal structure of VIRB8 from brucella suis

4AKZ · Type IV secretion system protein VIRB8: “Crystal structure of VIRB8 from brucella suis”. X-ray diffraction, 6 pockets (best druggability 0.84). MolNFT v1 #85718 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4AKZ
Type: protein
Length: 673 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Type IV secretion system protein VIRB8
UniProt: Q7CEG3
Pockets: 6 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Type IV secretion system protein VIRB8	protein	138	40% helix, 36% strand	Q7CEG3
B, C, E	Type IV secretion system protein VIRB8	protein	134	38% helix, 37% strand	Q7CEG3
D	Type IV secretion system protein VIRB8	protein	133	41% helix, 38% strand	Q7CEG3

Pockets

6 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	298	0.84	0.94	35	empty
2	1184	0.83	0.84	101	empty
3	1145	0.78	0.79	85	empty
4	66	0.34	0.77	14	empty
5	62	0.34	0.77	14	empty

Interfaces

6 interfaces between chains.

B–D · 886 Å² buried · 4 hydrogen bonds · protein-protein
C–E · 859 Å² buried · 4 hydrogen bonds · protein-protein
B–E · 806 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 655 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 425 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4AKZ · Crystal structure of VIRB8 from brucella suis · the same entry in another collection · chain E against E, 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 D 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 4AKZ · PDBe 4AKZ · UniProt Q7CEG3

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