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Structure of agrobacterium tumefaciens VIRB8 protein

Analyse Structure of agrobacterium tumefaciens VIRB8 protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2CC3
Type: protein
Length: 288 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein VIRB8
UniProt: P17798
Pockets: 3 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein VIRB8	protein	144	33% helix, 35% strand	P17798

Ligands and binding sites

MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	694	0.78	0.82	78	MPD
2	118	0.45	0.78	22	empty
3	70	0.34	0.75	20	empty

Interfaces

1 interface between chains.

A–B · 885 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

2CC3 · Structure of Agrobacterium tumefaciens VirB8 protein · the same entry in another collection · chain A against A, TM-score 1.00
P17798 · AlphaFold monomer V2.0 prediction for protein VIRB8 (P17798) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P17798
Elsewhere: RCSB PDB 2CC3 · PDBe 2CC3 · UniProt P17798

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