4ANP | pdb_00004anp

Crystal structure of human phenylalanine hydroxylase in complex with a pharmacological chaperone

• PDB DOI: https://doi.org/10.2210/pdb4ANP/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-03-21 Released: 2012-04-11 
• Deposition Author(s): Torreblanca, R., Lira-Navarrete, E., Sancho, J., Hurtado-Guerrero, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Structural and Mechanistic Basis of the Interaction between a Pharmacological Chaperone and Human Phenylalanine Hydroxylase.

Torreblanca, R., Lira-Navarrete, E., Sancho, J., Hurtado-Guerrero, R.

(2012) Chembiochem 13: 1266

• PubMed: 22549968 
• DOI: https://doi.org/10.1002/cbic.201200188


• PubMed Abstract: 
  

  Not without a chaperone: Pharmacological chaperones are designed to bind and ideally stabilise their target protein. Here, we elucidate the molecular mechanism of a potential pharmacological chaperone to treat phenylketonuria. The crystal structure of human phenylalanine hydroxylase with compound IV may help in the rational design of more efficient compounds to treat this disease.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular and Cellular Biology, Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit, Pedro Cerbuna 12, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Spain.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 37.9 kDa 
• Atom Count: 2,801 
• Modeled Residue Count: 309 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHENYLALANINE-4-HYDROXYLASE	A	324	Homo sapiens	Mutation(s): 0  EC: 1.14.16.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00439 (Homo sapiens) Explore P00439  Go to UniProtKB:  P00439
PHAROS:  P00439 GTEx:  ENSG00000171759

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3QI	C [auth A]	5,6-DIMETHYL-3-(4-METHYL-2-PYRIDINYL)-2-THIOXO-2,3-DIHYDROTHIENO[2,3- D]PYRIMIDIN-4(1H)-ONE C14 H13 N3 O S2 NYDQMBWQPMNQIZ-UHFFFAOYSA-N
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.283	α = 90
b = 107.511	β = 90
c = 124.55	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-11 
Deposition Author(s): Torreblanca, R., Lira-Navarrete, E., Sancho, J., Hurtado-Guerrero, R.

Revision History  

• Version 1.0: 2012-04-11
  Type: Initial release
  
• Version 1.1: 2012-07-25
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description