4PJ6

Crystal Structure of Human Insulin Regulated Aminopeptidase with Lysine in Active Site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Crystal structure of human insulin-regulated aminopeptidase with specificity for cyclic peptides.

Hermans, S.J.Ascher, D.B.Hancock, N.C.Holien, J.K.Michell, B.J.Yeen Chai, S.Morton, C.J.Parker, M.W.

(2015) Protein Sci 24: 190-199

  • DOI: https://doi.org/10.1002/pro.2604
  • Primary Citation of Related Structures:  
    4P8Q, 4PJ6

  • PubMed Abstract: 

    Insulin-regulated aminopeptidase (IRAP or oxytocinase) is a membrane-bound zinc-metallopeptidase that cleaves neuroactive peptides in the brain and produces memory enhancing effects when inhibited. We have determined the crystal structure of human IRAP revealing a closed, four domain arrangement with a large, mostly buried cavity abutting the active site. The structure reveals that the GAMEN exopeptidase loop adopts a very different conformation from other aminopeptidases, thus explaining IRAP's unique specificity for cyclic peptides such as oxytocin and vasopressin. Computational docking of a series of IRAP-specific cognitive enhancers into the crystal structure provides a molecular basis for their structure-activity relationships and demonstrates that the structure will be a powerful tool in the development of new classes of cognitive enhancers for treating a variety of memory disorders such as Alzheimer's disease.


  • Organizational Affiliation

    ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Melbourne, Victoria, 3065, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leucyl-cystinyl aminopeptidase
A, B
872Homo sapiensMutation(s): 0 
Gene Names: LNPEPOTASE
EC: 3.4.11.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIQ6 (Homo sapiens)
Explore Q9UIQ6 
Go to UniProtKB:  Q9UIQ6
PHAROS:  Q9UIQ6
GTEx:  ENSG00000113441 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UIQ6
Glycosylation
Glycosylation Sites: 7Go to GlyGen: Q9UIQ6-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
LYS
Query on LYS

Download Ideal Coordinates CCD File 
E [auth A],
N [auth B]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
M [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.031α = 90
b = 256.621β = 114.35
c = 71.31γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-03
    Type: Initial release
  • Version 1.1: 2015-02-11
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2023-12-27
    Changes: Data collection, Database references, Structure summary
  • Version 2.2: 2024-10-30
    Changes: Structure summary