› 3k5w

X-ray diffraction
2.6Å resolution

Crystal structure of a Carbohydrate kinase (YjeF family)from Helicobacter pylori

Released:
DOI: 10.2210/pdb3k5w/pdb
PDB entry 3k5w coloured by chain, front view.
PDB entry 3k5w coloured by chain, side view.
PDB entry 3k5w coloured by chain, top view.
Source organism: Helicobacter pylori
Entry authors: Satyanarayana L, Burley SK, Swaminathan S, New York SGX Research Center for Structural Genomics (NYSGXRC)

Function and Biology Details

Reactions catalysed: 
ADP + (6S)-6-beta-hydroxy-1,4,5,6-tetrahydronicotinamide adenine-dinucleotide = AMP + phosphate + NADH
(6R)-6-beta-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide = (6S)-6-beta-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo tetramer
homo octamer
Assembly name:
PDBe Complex ID:
PDB-CPX-157407 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Bifunctional NAD(P)H-hydrate repair enzyme Nnr Chain: A
Molecule details ›
Chain: A
Length: 475 amino acids
Theoretical weight: 52.41 KDa
Source organism: Helicobacter pylori
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P56176 (Residues: 2-466; Coverage: 100%)
Gene names: HP_1363, nnr
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand PO4 1 x PO4
1 modified residue:
Ligand MSE 8 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: I422
Unit cell:
a: 119.955Å b: 119.955Å c: 162.226Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.233 0.233 0.262
Expression system: Escherichia coli BL21(DE3)

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