5AMA

Crystal structure of the Angiotensin-1 converting enzyme N-domain in complex with amyloid-beta 1-16

PDB DOI: https://doi.org/10.2210/pdb5AMA/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): Yes

Deposited: 2015-03-10 Released: 2016-01-13
Deposition Author(s): Masuyer, G., Larmuth, K.M., Douglas, R.G., Sturrock, E.D., Acharya, K.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.218
R-Value Work: 0.187
R-Value Observed: 0.188

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: 299.94 kDa
Atom Count: 22,267
Modelled Residue Count: 2,424
Deposited Residue Count: 2,516
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, C, D	629	Homo sapiens	Mutation(s): 9 EC: 3.4.15.1
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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, H, K	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain H Focus chain K Interactions & Density Focus chain E Focus chain F Focus chain H Focus chain K
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, J, M	2		N-Glycosylation	Interactions Focus chain G Focus chain J Focus chain M Interactions & Density Focus chain G Focus chain J Focus chain M
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	3		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	L	4		N-Glycosylation	Interactions Focus chain L Interactions & Density Focus chain L
Glycosylation Resources
GlyTouCan: G86566TX GlyCosmos: G86566TX GlyGen: G86566TX

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-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	N	4		N-Glycosylation	Interactions Focus chain N Interactions & Density Focus chain N
Glycosylation Resources
GlyTouCan: G47477HI GlyCosmos: G47477HI GlyGen: G47477HI

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain V [auth A] SDF format, chain MA [auth C] SDF format, chain TA [auth D] SDF format, chain VA [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain TA [auth D] MOL2 format, chain VA [auth D]	EA [auth B] FA [auth B] MA [auth C] TA [auth D] V [auth A] EA [auth B], FA [auth B], MA [auth C], TA [auth D], V [auth A], VA [auth D]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain FA [auth B] Focus chain MA [auth C] Focus chain TA [auth D] Focus chain V [auth A] Focus chain VA [auth D] Interactions & Density Focus chain EA [auth B] Focus chain FA [auth B] Focus chain MA [auth C] Focus chain TA [auth D] Focus chain V [auth A] Focus chain VA [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain RA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth D]	RA [auth D], S [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain RA [auth D] Focus chain S [auth A] Interactions & Density Focus chain RA [auth D] Focus chain S [auth A]
ASP Query on ASP Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain X [auth B] SDF format, chain GA [auth C] SDF format, chain NA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain X [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain NA [auth D]	GA [auth C], NA [auth D], O [auth A], X [auth B]	ASPARTIC ACID C₄ H₇ N O₄ CKLJMWTZIZZHCS-REOHCLBHSA-N		Interactions Focus chain GA [auth C] Focus chain NA [auth D] Focus chain O [auth A] Focus chain X [auth B] Interactions & Density Focus chain GA [auth C] Focus chain NA [auth D] Focus chain O [auth A] Focus chain X [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain KA [auth C] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain UA [auth D] SDF format, chain W [auth A] SDF format, chain DA [auth B] SDF format, chain LA [auth C] SDF format, chain SA [auth D] SDF format, chain WA [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth D] MOL2 format, chain W [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain LA [auth C] MOL2 format, chain SA [auth D] MOL2 format, chain WA [auth D]	BA [auth B] CA [auth B] DA [auth B] KA [auth C] LA [auth C] BA [auth B], CA [auth B], DA [auth B], KA [auth C], LA [auth C], SA [auth D], T [auth A], U [auth A], UA [auth D], W [auth A], WA [auth D]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain SA [auth D] Focus chain T [auth A] Focus chain U [auth A] Focus chain UA [auth D] Focus chain W [auth A] Focus chain WA [auth D] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain SA [auth D] Focus chain T [auth A] Focus chain U [auth A] Focus chain UA [auth D] Focus chain W [auth A] Focus chain WA [auth D]
SER Query on SER Download Ideal Coordinates CCD File SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain Y [auth B] SDF format, chain HA [auth C] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain HA [auth C]	HA [auth C], OA [auth D], P [auth A], Y [auth B]	SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-REOHCLBHSA-N		Interactions Focus chain HA [auth C] Focus chain OA [auth D] Focus chain P [auth A] Focus chain Y [auth B] Interactions & Density Focus chain HA [auth C] Focus chain OA [auth D] Focus chain P [auth A] Focus chain Y [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain PA [auth D] SDF format, chain Q [auth A] SDF format, chain Z [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain Z [auth B]	IA [auth C], PA [auth D], Q [auth A], Z [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain IA [auth C] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain Z [auth B] Interactions & Density Focus chain IA [auth C] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain Z [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain AA [auth B] SDF format, chain JA [auth C] SDF format, chain QA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain JA [auth C] MOL2 format, chain QA [auth D]	AA [auth B], JA [auth C], QA [auth D], R [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain JA [auth C] Focus chain QA [auth D] Focus chain R [auth A] Interactions & Density Focus chain AA [auth B] Focus chain JA [auth C] Focus chain QA [auth D] Focus chain R [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.218
R-Value Work: 0.187
R-Value Observed: 0.188
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.34	α = 85.09
b = 101.73	β = 85.62
c = 114.14	γ = 81.3

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-01-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-01-13
Type: Initial release
Version 1.1: 2016-01-20
Changes: Database references
Version 1.2: 2016-04-06
Changes: Database references
Version 1.3: 2018-06-20
Changes: Advisory, Data collection, Derived calculations
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary