2H5G

Crystal structure of human pyrroline-5-carboxylate synthetase

• PDB DOI: https://doi.org/10.2210/pdb2H5G/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-05-26 Released: 2006-06-23 
• Deposition Author(s): Papagrigoriou, E., Shafqat, N., Turnbull, A.P., Berridge, G., Hozjan, V., Kavanagh, K., Gileadi, O., Smee, C., Bray, J., Gorrec, F., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.272 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 

Literature

Crystal structure of human pyrroline-5-carboxylate synthetase

Papagrigoriou, E., Shafqat, N., Turnbull, A.P., Berridge, G., Hozjan, V., Kavanagh, K., Gileadi, O., Smee, C., Bray, J., Gorrec, F., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A., Oppermann, U.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 104.05 kDa 
• Atom Count: 6,695 
• Modelled Residue Count: 842 
• Deposited Residue Count: 926 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Delta 1-pyrroline-5-carboxylate synthetase	A, B	463	Homo sapiens	Mutation(s): 6  Gene Names: ALDH18A1 EC: 1.2.1.41 (PDB Primary Data), 2.7.2.11 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P54886 (Homo sapiens) Explore P54886  Go to UniProtKB:  P54886
PHAROS:  P54886 GTEx:  ENSG00000059573

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.272 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.022	α = 90
b = 137.402	β = 90
c = 72.057	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-23 
Deposition Author(s): Papagrigoriou, E., Shafqat, N., Turnbull, A.P., Berridge, G., Hozjan, V., Kavanagh, K., Gileadi, O., Smee, C., Bray, J., Gorrec, F., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2006-06-23
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary