› 5m6d

X-ray diffraction
2Å resolution

Streptococcus pneumoniae Glyceraldehyde-3-Phosphate Dehydrogenase (SpGAPDH) crystal structure

Released:
DOI: 10.2210/pdb5m6d/pdb
PDB entry 5m6d coloured by chain, front view.
PDB entry 5m6d coloured by chain, side view.
PDB entry 5m6d coloured by chain, top view.
Source organism: Streptococcus pneumoniae
Primary publication:
Deciphering Key Residues Involved in the Virulence-promoting Interactions between Streptococcus pneumoniae and Human Plasminogen.
Moreau C, Terrasse R, Thielens NM, Vernet T, Gaboriaud C, Di Guilmi AM
J Biol Chem 292 2217-2225 (2017)
PMID: 28011643

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-125127 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glyceraldehyde-3-phosphate dehydrogenase Chains: A, B
Molecule details ›
Chains: A, B
Length: 355 amino acids
Theoretical weight: 38.44 KDa
Source organism: Streptococcus pneumoniae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: I6L8L9 (Residues: 2-335; Coverage: 100%)
Gene names: AZJ28_04050, ERS019420_02001, ERS096071_02139, GM530_10330, GM537_10140, GM539_10415, SAMEA104154639_02274, SAMEA3172940_02100, SAMEA3233211_01979, SAMEA3353485_01051, SAMEA3353631_02382, SAMEA3354366_01907, gap, gapA, gapdh
Sequence domains:
Structure domains: Dihydrodipicolinate Reductase; domain 2

Ligands and Environments

4 bound ligands:
Ligand CL 2 x CL
Ligand CA 1 x CA
Ligand ACY 2 x ACY
Ligand GOL 3 x GOL
1 modified residue:
Ligand CSU 2 x CSU

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: C2
Unit cell:
a: 81.041Å b: 130.237Å c: 79.837Å
α: 90° β: 119.64° γ: 90°
R-values:
R R work R free
0.196 0.195 0.215
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Plasminogen-binding proteins as an evasion mechanism of the host's innate immunity in infectious diseases.
Ayón-Núñez et al. (2018)
7 other articles

2 mentions without citation

Deciphering Key Residues Involved in the Virulence-promoting Interactions between Streptococcus pneumoniae and Human Plasminogen.
Moreau et al. (2017)
1 more