2XHM | pdb_00002xhm

Crystal structure of AnCE-K26 complex

PDB DOI: https://doi.org/10.2210/pdb2XHM/pdb

Classification: HYDROLASE
Organism(s): Drosophila melanogaster
Expression System: Komagataella phaffii GS115
Mutation(s): No

Deposited: 2010-06-18 Released: 2010-07-14
Deposition Author(s): Akif, M., Ntai, I., Sturrock, E.D., Isaac, R.E., Bachmann, B.O., Acharya, K.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.215 (Depositor), 0.220 (DCC)
R-Value Work:
0.194 (Depositor), 0.196 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal Structure of a Phosphonotripeptide K-26 in Complex with Angiotensin Converting Enzyme Homologue (Ance) from Drosophila Melanogaster.

Akif, M., Ntai, I., Sturrock, E.D., Isaac, R.E., Bachmann, B.O., Acharya, K.R.

(2010) Biochem Biophys Res Commun 398: 532

PubMed: 20599761 Search on PubMed
DOI: https://doi.org/10.1016/j.bbrc.2010.06.113
Primary Citation Related Structures:
2XHM

PubMed Abstract:
Angiotensin-I converting enzyme (ACE, a zinc dependent dipeptidyl carboxypeptidase) is a major target of drugs due to its role in the modulation of blood pressure and cardiovascular disorders. Here we present a crystal structure of AnCE (an ACE homologue from Drosophila melanogaster with a single enzymatic domain) in complex with a natural product-phosphonotripeptide, K-26 at 1.96A resolution. The inhibitor binds exclusively in the S(1) and S(2) binding pockets of AnCE (coordinating the zinc ion) through ionic and hydrogen bond interactions. A detailed structural comparison of AnCE.K-26 complex with individual domains of human somatic ACE provides useful information for further exploration of ACE inhibitor pharmacophores involving phosphonic acids.

Organizational Affiliation

Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK.

Macromolecule Content

Total Structure Weight: 71.51 kDa
Atom Count: 5,532
Modeled Residue Count: 598
Deposited Residue Count: 598
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ANGIOTENSIN CONVERTING ENZYME	A	598	Drosophila melanogaster	Mutation(s): 0 EC: 3.4.15.1
UniProt
Find proteins for Q10714 (Drosophila melanogaster) Explore Q10714 Go to UniProtKB: Q10714
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q10714
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A	Go to GlyGen: Q10714-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	6		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G64803HZ GlyCosmos: G64803HZ GlyGen: G64803HZ

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K26 Query on K26 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	N-ACETYL-L-ILE-L-TYR-(R)-1-AMINO-2-(4-HYDROXYPHENYL)ETHYLPHOSPHONIC ACID C₂₅ H₃₄ N₃ O₈ P ZFRNBYWFOLDQKG-FDMHNHSTSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.215 (Depositor), 0.220 (DCC)
R-Value Work: 0.194 (Depositor), 0.196 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.707	α = 90
b = 172.707	β = 90
c = 101.696	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-07-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-07-14
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-16
Changes: Structure summary