6ZPQ | pdb_00006zpq

Crystal structure of the open conformation of Angiotensin-1 converting enzyme N-domain.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.214 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Angiotensin-converting enzyme open for business: structural insights into the subdomain dynamics.

Cozier, G.E.Lubbe, L.Sturrock, E.D.Acharya, K.R.

(2021) FEBS J 288: 2238-2256

  • DOI: https://doi.org/10.1111/febs.15601
  • Primary Citation Related Structures: 
    6ZPQ, 6ZPT, 6ZPU

  • PubMed Abstract: 

    Angiotensin-1-converting enzyme (ACE) is a key enzyme in the renin-angiotensin-aldosterone and kinin systems where it cleaves angiotensin I and bradykinin peptides, respectively. However, ACE also participates in numerous other physiological functions, can hydrolyse many peptide substrates and has various exo- and endopeptidase activities. ACE achieves this complexity by containing two homologous catalytic domains (N- and C-domains), which exhibit different substrate specificities. Here, we present the first open conformation structures of ACE N-domain and a unique closed C-domain structure (2.0 Å) where the C terminus of a symmetry-related molecule is observed inserted into the active-site cavity and binding to the zinc ion. The open native N-domain structure (1.85 Å) enables comparison with ACE2, a homologue previously observed in open and closed states. An open S 2 _S'-mutant N-domain structure (2.80 Å) includes mutated residues in the S 2 and S' subsites that effect ligand binding, but are distal to the binding site. Analysis of these structures provides important insights into how structural features of the ACE domains are able to accommodate the wide variety of substrates and allow different peptidase activities. DATABASE: The atomic coordinates and structure factors for Open nACE, Open S2_S'-nACE and Native G13-cACE structures have been deposited with codes 6ZPQ, 6ZPT and 6ZPU, respectively, in the RCSB Protein Data Bank, www.pdb.org.


  • Organizational Affiliation
    • Department of Biology and Biochemistry, University of Bath, Bath, UK.

Macromolecule Content 

  • Total Structure Weight: 298.37 kDa 
  • Atom Count: 22,243 
  • Modeled Residue Count: 2,425 
  • Deposited Residue Count: 2,516 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Angiotensin-converting enzyme
A, B, C, D
629Homo sapiensMutation(s): 8 
Gene Names: ACEDCPDCP1
EC: 3.2.1 (PDB Primary Data), 3.4.15.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P12821 (Homo sapiens)
Explore P12821 
Go to UniProtKB:  P12821
PHAROS:  P12821
GTEx:  ENSG00000159640 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12821
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P12821-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, H, J
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
F, G, I, K
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB
GlyCosmos: G21290RB
GlyGen: G21290RB

Small Molecules

Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
CA [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
BCN

Query on BCN



Download:Ideal Coordinates CCD File
DB [auth D],
EA [auth B],
M [auth A],
O [auth A],
SA [auth C]
BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
EB [auth D],
GA [auth B],
HA [auth B],
R [auth A],
V [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
FA [auth B],
LA [auth B],
MA [auth B],
P [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
MXE

Query on MXE



Download:Ideal Coordinates CCD File
KA [auth B],
TA [auth C]
2-METHOXYETHANOL
C3 H8 O2
XNWFRZJHXBZDAG-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
LB [auth D],
NA [auth B],
Y [auth A],
YA [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
FB [auth D]
GB [auth D]
HB [auth D]
IA [auth B]
IB [auth D]
FB [auth D],
GB [auth D],
HB [auth D],
IA [auth B],
IB [auth D],
JA [auth B],
Q [auth A],
T [auth A],
U [auth A],
VA [auth C],
W [auth A],
WA [auth C],
X [auth A],
XA [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
BO3

Query on BO3



Download:Ideal Coordinates CCD File
CB [auth D]
DA [auth B]
JB [auth D]
KB [auth D]
L [auth A]
CB [auth D],
DA [auth B],
JB [auth D],
KB [auth D],
L [auth A],
N [auth A],
S [auth A],
UA [auth C]
BORIC ACID
B H3 O3
KGBXLFKZBHKPEV-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
BA [auth A],
BB [auth C],
NB [auth D],
QA [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
MB [auth D],
OA [auth B],
Z [auth A],
ZA [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
AA [auth A],
AB [auth C],
PA [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
RA [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.214 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.683α = 97.756
b = 99.934β = 90.206
c = 128.701γ = 111.057
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/M026647/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-28
    Type: Initial release
  • Version 1.1: 2021-04-14
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary