6F9V

Crystal structure of human Angiotensin-1 converting enzyme N-domain in complex with Sampatrilat.

PDB DOI: https://doi.org/10.2210/pdb6F9V/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2017-12-15 Released: 2018-03-07
Deposition Author(s): Cozier, G.E., Acharya, K.R.
Funding Organization(s): Medical Research Council (United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.212
R-Value Work: 0.183
R-Value Observed: 0.184

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 150.52 kDa
Atom Count: 12,014
Modelled Residue Count: 1,209
Deposited Residue Count: 1,258
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme	A, B	629	Homo sapiens	Mutation(s): 0 Gene Names: ACE, DCP, DCP1 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P12821
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	5		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G00395TQ GlyCosmos: G00395TQ GlyGen: G00395TQ

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D0Z Query on D0Z Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain R [auth B] MOL2 format, chain F [auth A] MOL2 format, chain R [auth B]	F [auth A], R [auth B]	Sampatrilat C₂₆ H₄₀ N₄ O₉ S LPUDGHQMOAHMMF-JBACZVJFSA-N		Interactions Focus chain F [auth A] Focus chain R [auth B] Interactions & Density Focus chain F [auth A] Focus chain R [auth B]
P33 Query on P33 Download Ideal Coordinates CCD File SDF format, chain FA [auth B] MOL2 format, chain FA [auth B]	FA [auth B]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C₁₄ H₃₀ O₈ XPJRQAIZZQMSCM-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Interactions & Density Focus chain FA [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain I [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain I [auth A]	I [auth A], U [auth B], V [auth B], W [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain I [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A]	P [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B]	CA [auth B], DA [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain O [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain O [auth A]	EA [auth B], O [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain O [auth A] Interactions & Density Focus chain EA [auth B] Focus chain O [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain Q [auth B] MOL2 format, chain E [auth A] MOL2 format, chain Q [auth B]	E [auth A], Q [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain Q [auth B] Interactions & Density Focus chain E [auth A] Focus chain Q [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] L [auth A] M [auth A] N [auth A] AA [auth B], BA [auth B], L [auth A], M [auth A], N [auth A], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B]	G [auth A], H [auth A], S [auth B], T [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain S [auth B] Focus chain T [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain X [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain X [auth B]	J [auth A], K [auth A], X [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain X [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain X [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
D0Z	Binding MOAD: 6F9V	Ki: 171.9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.212
R-Value Work: 0.183
R-Value Observed: 0.184
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.224	α = 88.36
b = 77.215	β = 64.2
c = 83.107	γ = 75.29

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-03-07

Deposition Author(s):

Cozier, G.E.

Acharya, K.R.

Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MR/M026647/1

Revision History (Full details and data files)

Version 1.0: 2018-03-07
Type: Initial release
Version 1.1: 2018-03-21
Changes: Database references
Version 1.2: 2018-05-02
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary