5LHD

Structure of glycosylated human aminopeptidase N

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history. 


Literature

Allosteric inhibition of aminopeptidase N functions related to tumor growth and virus infection.

Santiago, C., Mudgal, G., Reguera, J., Recacha, R., Albrecht, S., Enjuanes, L., Casasnovas, J.M.

(2017) Sci Rep 7: 46045-46045

  • DOI: 10.1038/srep46045
  • Primary Citation of Related Structures:  
    5LDS, 5LG6, 5LHD

  • PubMed Abstract: 

    • Cell surface aminopeptidase N (APN) is a membrane-bound ectoenzyme that hydrolyzes proteins and peptides and regulates numerous cell functions. APN participates in tumor cell expansion and motility, and is a target for cancer therapies. Small drugs that bind to the APN active site inhibit catalysis and suppress tumor growth ...

    Cell surface aminopeptidase N (APN) is a membrane-bound ectoenzyme that hydrolyzes proteins and peptides and regulates numerous cell functions. APN participates in tumor cell expansion and motility, and is a target for cancer therapies. Small drugs that bind to the APN active site inhibit catalysis and suppress tumor growth. APN is also a major cell entry receptor for coronavirus, which binds to a region distant from the active site. Three crystal structures that we determined of human and pig APN ectodomains defined the dynamic conformation of the protein. These structures offered snapshots of closed, intermediate and open APN, which represent distinct functional states. Coronavirus envelope proteins specifically recognized the open APN form, prevented ectodomain progression to the closed form and substrate hydrolysis. In addition, drugs that bind the active site inhibited both coronavirus binding to cell surface APN and infection; the drugs probably hindered APN transition to the virus-specific open form. We conclude that allosteric inhibition of APN functions occurs by ligand suppression of ectodomain motions necessary for catalysis and virus cell entry, as validated by locking APN with disulfides. Blocking APN dynamics can thus be a valuable approach to development of drugs that target this ectoenzyme.

    Organizational Affiliation: 

    Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aminopeptidase NA, B, C, D950Homo sapiensMutation(s): 0 
Gene Names: ANPEP, APN, CD13, PEPN
EC: 3.4.11.2
UniProt & NIH Common Fund Data Resources
Find proteins for P15144 (Homo sapiens)
Explore P15144 
Go to UniProtKB:  P15144
PHAROS:  P15144
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15144
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE, J, K, R 4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G40894EI
GlyCosmos:  G40894EI
GlyGen:  G40894EI
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseF, L, S 5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G89225LT
GlyCosmos:  G89225LT
GlyGen:  G89225LT
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
DA [auth d],
EA [auth e],
FA [auth f],
G,
GA [auth g],
DA [auth d],
EA [auth e],
FA [auth f],
G,
GA [auth g],
I,
M,
N,
P,
Q,
V,
X
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth b],
CA [auth c],
H,
O,
U,
BA [auth b],
CA [auth c],
H,
O,
U,
Z
3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseT 4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G31886NL
GlyCosmos:  G31886NL
GlyGen:  G31886NL
Entity ID: 7
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseAA [auth a],
W		6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G67849DJ
GlyCosmos:  G67849DJ
GlyGen:  G67849DJ
Entity ID: 8
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseY 6N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G36782MK
GlyCosmos:  G36782MK
GlyGen:  G36782MK
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
BB [auth B],
DC [auth D],
EC [auth D],
HA [auth A],
IA [auth A],
BB [auth B],
DC [auth D],
EC [auth D],
HA [auth A],
IA [auth A],
PB [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
CB [auth B],
FC [auth D],
JA [auth A],
QB [auth C]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AB [auth A],
AC [auth C],
BC [auth C],
CC [auth C],
DB [auth B],
AB [auth A],
AC [auth C],
BC [auth C],
CC [auth C],
DB [auth B],
EB [auth B],
FB [auth B],
GB [auth B],
GC [auth D],
HB [auth B],
HC [auth D],
IB [auth B],
IC [auth D],
JB [auth B],
JC [auth D],
KA [auth A],
KB [auth B],
KC [auth D],
LA [auth A],
LB [auth B],
MA [auth A],
MB [auth B],
NA [auth A],
NB [auth B],
OA [auth A],
OB [auth B],
PA [auth A],
QA [auth A],
RA [auth A],
RB [auth C],
SA [auth A],
SB [auth C],
TA [auth A],
TB [auth C],
UA [auth A],
UB [auth C],
VA [auth A],
VB [auth C],
WA [auth A],
WB [auth C],
XA [auth A],
XB [auth C],
YA [auth A],
YB [auth C],
ZA [auth A],
ZB [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.093α = 90
b = 168.856β = 90
c = 244.249γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Spanish Ministry of ScienceSpainBFU2011-23940 and BIO2014-52683-R

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-04-19
    Changes: Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary