4ANP

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.237
R-Value Work: 0.204
R-Value Observed: 0.205

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1002/cbic.201200188
Primary Citation of Related Structures:
4ANP

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.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00439
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3QI Query on 3QI Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	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		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
3QI	Binding MOAD: 4ANP	Ki: 2.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.237
R-Value Work: 0.204
R-Value Observed: 0.205
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-04-11

Deposition Author(s):

Revision History (Full details and data files)

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