5L44 | pdb_00005l44

Structure of K-26-DCP in complex with the K-26 tripeptide

PDB DOI: https://doi.org/10.2210/pdb5L44/pdb

Classification: HYDROLASE
Organism(s): Astrosporangium hypotensionis K-26
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-05-24 Released: 2016-10-26
Deposition Author(s): Masuyer, G., Acharya, K.R., Kramer, G.J., Bachmann, B.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.213 (Depositor), 0.238 (DCC)
R-Value Work:
0.185 (Depositor)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of a peptidyl-dipeptidase K-26-DCP from Actinomycete in complex with its natural inhibitor.

Masuyer, G., Cozier, G.E., Kramer, G.J., Bachmann, B.O., Acharya, K.R.

(2016) FEBS J 283: 4357-4369

PubMed: 27754586 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1111/febs.13928
Primary Citation Related Structures:
5L43, 5L44

PubMed Abstract:
Several soil-derived Actinobacteria produce secondary metabolites that are proven specific and potent inhibitors of the human angiotensin-I-converting enzyme (ACE), a key target for the modulation of hypertension through its role in the renin-angiotensin-aldosterone system. K-26-DCP is a zinc dipeptidyl carboxypeptidase (DCP) produced by Astrosporangium hypotensionis, and an ancestral homologue of ACE. Here we report the high-resolution crystal structures of K-26-DCP and of its complex with the natural microbial tripeptide product K-26. The experimental results provide the structural basis for better understanding the specificity of K-26 for human ACE over bacterial DCPs. Structural data are available in the PDB under the accession numbers 5L43 and 5L44.

Organizational Affiliation

Department of Biology and Biochemistry, University of Bath, UK.

Macromolecule Content

Total Structure Weight: 154.68 kDa
Atom Count: 11,677
Modeled Residue Count: 1,324
Deposited Residue Count: 1,366
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
K-26 dipeptidyl carboxypeptidase	A, B	683	Astrosporangium hypotensionis K-26	Mutation(s): 0 EC: 3.4.15.5
UniProt
Find proteins for A0A1L1QK30 (Astrosporangium hypotensionis K-26) Explore A0A1L1QK30 Go to UniProtKB: A0A1L1QK30
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1L1QK30
Sequence Annotations Expand
Reference Sequence

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 G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	G [auth A], L [auth B]	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 G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B]	F [auth A], K [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth A], I [auth B], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.213 (Depositor), 0.238 (DCC)
R-Value Work: 0.185 (Depositor)
R-Value Observed: 0.187 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.58	α = 97.72
b = 66.94	β = 90.71
c = 102	γ = 117.37

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-10-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-10-26
Type: Initial release
Version 1.1: 2016-11-02
Changes: Database references
Version 1.2: 2016-12-14
Changes: Database references
Version 1.3: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description