6F9R

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

PDB DOI: https://doi.org/10.2210/pdb6F9R/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: 1.85 Å
R-Value Free: 0.228
R-Value Work: 0.198
R-Value Observed: 0.199

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: 151.09 kDa
Atom Count: 11,475
Modelled Residue Count: 1,211
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-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	D, G	4		N-Glycosylation	Interactions Focus chain D Focus chain G Interactions & Density Focus chain D Focus chain G
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F	2		N-Glycosylation	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
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	H	3		N-Glycosylation	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D0W Query on D0W Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain S [auth B]	J [auth A], S [auth B]	Sampatrilat-Asp C₂₅ H₃₃ N₃ O₁₀ ZQIWHIVXBQEYTN-WDSOQIARSA-N		Interactions Focus chain J [auth A] Focus chain S [auth B] Interactions & Density Focus chain J [auth A] Focus chain S [auth B]
PE8 Query on PE8 Download Ideal Coordinates CCD File SDF format, chain CA [auth B] MOL2 format, chain CA [auth B]	CA [auth B]	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL C₁₆ H₃₄ O₉ GLZWNFNQMJAZGY-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Interactions & Density Focus chain CA [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A]	M [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain L [auth A] SDF format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain L [auth A] MOL2 format, chain U [auth B]	L [auth A], U [auth B], V [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain L [auth A] Focus chain U [auth B] Focus chain V [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain R [auth B] MOL2 format, chain I [auth A] MOL2 format, chain R [auth B]	I [auth A], R [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain R [auth B] Interactions & Density Focus chain I [auth A] Focus chain R [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 Y [auth B] SDF format, chain O [auth A] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain O [auth A] MOL2 format, chain Z [auth B]	AA [auth B], BA [auth B], O [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 O [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 O [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A]	P [auth A], Q [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain P [auth A] Focus chain Q [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain K [auth A] MOL2 format, chain T [auth B] MOL2 format, chain K [auth A]	K [auth A], T [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain T [auth B] Interactions & Density Focus chain K [auth A] Focus chain T [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain N [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B]	N [auth A], W [auth B], X [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain N [auth A] Focus chain W [auth B] Focus chain X [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
D0W	Binding MOAD: 6F9R	Ki: 1.06e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.228
R-Value Work: 0.198
R-Value Observed: 0.199
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.591	α = 88.43
b = 76.966	β = 64.4
c = 82.637	γ = 75.32

Software Package:

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

Structure Validation

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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

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Help and Resources

6F9R

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)