› 3w6u

X-ray diffraction
2Å resolution

Crystal structure of NADP bound L-serine 3-dehydrogenase from Hyperthermophilic Archaeon Pyrobaculum calidifontis

Released:
DOI: 10.2210/pdb3w6u/pdb
PDB entry 3w6u coloured by chain, front view.
PDB entry 3w6u coloured by chain, side view.
PDB entry 3w6u coloured by chain, top view.
Source organism: Pyrobaculum calidifontis JCM 11548
Primary publication:
Crystal structure of the NADP+ and tartrate-bound complex of L-serine 3-dehydrogenase from the hyperthermophilic archaeon Pyrobaculum calidifontis.
Yoneda K, Sakuraba H, Araki T, Ohshima T
Extremophiles 22 395-405 (2018)
PMID: 29353380

Function and Biology Details

Reaction catalysed: 
(1a) L-serine + NADP(+) = 2-aminomalonate semialdehyde + NADPH
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-107180 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
6-phosphogluconate dehydrogenase, NAD-binding protein Chain: A
Molecule details ›
Chain: A
Length: 306 amino acids
Theoretical weight: 33.44 KDa
Source organism: Pyrobaculum calidifontis JCM 11548
Expression system: Escherichia coli
UniProt:
  • Canonical: A3MU08 (Residues: 1-286; Coverage: 100%)
Gene name: Pcal_0699
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NAP 1 x NAP
No bound ligands
1 modified residue:
Ligand MSE 13 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-1A
Spacegroup: C2
Unit cell:
a: 121.603Å b: 56.827Å c: 56.571Å
α: 90° β: 106.69° γ: 90°
R-values:
R R work R free
0.227 0.227 0.242
Expression system: Escherichia coli

Quick links