› 6r1b

X-ray diffraction
2.27Å resolution

Crystal structure of UgpB from Mycobacterium tuberculosis in complex with glycerophosphocholine

Released:
DOI: 10.2210/pdb6r1b/pdb
PDB entry 6r1b coloured by chain, front view.
PDB entry 6r1b coloured by chain, side view.
PDB entry 6r1b coloured by chain, top view.
Source organism: Mycobacterium tuberculosis
Primary publication:
Structural Basis of Glycerophosphodiester Recognition by the Mycobacterium tuberculosis Substrate-Binding Protein UgpB.
Fenn JS, Nepravishta R, Guy CS, Harrison J, Angulo J, Cameron AD, Fullam E
ACS Chem Biol 14 1879-1887 (2019)
PMID: 31433162

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159807 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Probable Sn-glycerol-3-phosphate-binding lipoprotein UgpB Chain: A
Molecule details ›
Chain: A
Length: 394 amino acids
Theoretical weight: 42.81 KDa
Source organism: Mycobacterium tuberculosis
Expression system: Mycolicibacterium smegmatis
UniProt:
  • Canonical: P71619 (Residues: 36-429; Coverage: 90%)
Gene names: Rv2833c, ugpB
Sequence domains: Bacterial extracellular solute-binding protein
Probable Sn-glycerol-3-phosphate-binding lipoprotein UgpB Chain: B
Molecule details ›
Chain: B
Length: 395 amino acids
Theoretical weight: 42.87 KDa
Source organism: Mycobacterium tuberculosis
Expression system: Mycolicibacterium smegmatis
UniProt:
  • Canonical: P71619 (Residues: 35-429; Coverage: 91%)
Gene names: Rv2833c, ugpB
Sequence domains: Bacterial extracellular solute-binding protein
Probable Sn-glycerol-3-phosphate-binding lipoprotein UgpB Chain: C
Molecule details ›
Chain: C
Length: 384 amino acids
Theoretical weight: 41.66 KDa
Source organism: Mycobacterium tuberculosis
Expression system: Mycolicibacterium smegmatis
UniProt:
  • Canonical: P71619 (Residues: 35-430; Coverage: 88%)
Gene names: Rv2833c, ugpB
Sequence domains: Bacterial extracellular solute-binding protein
Probable Sn-glycerol-3-phosphate-binding lipoprotein UgpB Chain: D
Molecule details ›
Chain: D
Length: 382 amino acids
Theoretical weight: 41.37 KDa
Source organism: Mycobacterium tuberculosis
Expression system: Mycolicibacterium smegmatis
UniProt:
  • Canonical: P71619 (Residues: 35-428; Coverage: 88%)
Gene names: Rv2833c, ugpB
Sequence domains: Bacterial extracellular solute-binding protein

Ligands and Environments

3 bound ligands:
Ligand CH5 4 x CH5
Ligand MG 5 x MG
Ligand GOL 4 x GOL
1 modified residue:
Ligand MLZ 4 x MLZ

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P212121
Unit cell:
a: 46.11Å b: 169.86Å c: 213.31Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.206 0.256
Expression system: Mycolicibacterium smegmatis

Quick links

Citations

1 review citation

Transporters Involved in the Biogenesis and Functionalization of the Mycobacterial Cell Envelope.
Jackson et al. (2021)
4 other articles

4 mentions without citation

The ATP-Binding Cassette (ABC) Transport Systems in Mycobacterium tuberculosis: Structure, Function, and Possible Targets for Therapeutics.
Cassio Barreto de Oliveira et al. (2020)
3 more