4DYO

Crystal Structure of Human Aspartyl Aminopeptidase (DNPEP) in complex with Aspartic acid Hydroxamate

• PDB DOI: https://doi.org/10.2210/pdb4DYO/pdb
• Entry: 4DYO supersedes: 3L6S

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


• Deposited: 2012-02-29 Released: 2012-03-14 
• Deposition Author(s): Chaikuad, A., Pilka, E., Vollmar, M., Krojer, T., Muniz, J.R.C., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Kavanagh, K.L., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.195 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 

Literature

Structure of human aspartyl aminopeptidase complexed with substrate analogue: insight into catalytic mechanism, substrate specificity and M18 peptidase family.

Chaikuad, A., Pilka, E.S., Riso, A.D., Delft, F.V., Kavanagh, K.L., Venien-Bryan, C., Oppermann, U., Yue, W.W.

(2012) BMC Struct Biol 12: 14-14

• PubMed: 22720794 
• DOI: https://doi.org/10.1186/1472-6807-12-14
• Primary Citation of Related Structures:  
  4DYO


• PubMed Abstract: 
  

  Aspartyl aminopeptidase (DNPEP), with specificity towards an acidic amino acid at the N-terminus, is the only mammalian member among the poorly understood M18 peptidases. DNPEP has implicated roles in protein and peptide metabolism, as well as the renin-angiotensin system in blood pressure regulation. Despite previous enzyme and substrate characterization, structural details of DNPEP regarding ligand recognition and catalytic mechanism remain to be delineated.

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Organizational Affiliation: 

Structural Genomics Consortium, Old Road Research Campus Building, Oxford OX3 7DQ, UK.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 54.42 kDa 
• Atom Count: 3,955 
• Modelled Residue Count: 457 
• Deposited Residue Count: 485 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartyl aminopeptidase	A	485	Homo sapiens	Mutation(s): 0  Gene Names: ASPEP, DAP, DNPEP EC: 3.4.11.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULA0 (Homo sapiens) Explore Q9ULA0  Go to UniProtKB:  Q9ULA0
PHAROS:  Q9ULA0 GTEx:  ENSG00000123992

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SD4	E [auth A]	N-hydroxy-L-asparagine C4 H8 N2 O4 ZBYVTTSIVDYQSO-REOHCLBHSA-N
GOL	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.195 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 
• Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 244.595	α = 90
b = 244.595	β = 90
c = 244.595	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-14 
Deposition Author(s): Chaikuad, A., Pilka, E., Vollmar, M., Krojer, T., Muniz, J.R.C., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Kavanagh, K.L., Oppermann, U., Structural Genomics Consortium (SGC)
• This entry supersedes: 3L6S

Revision History  

• Version 1.0: 2012-03-14
  Type: Initial release
  
• Version 1.1: 2012-07-18
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection