4Z7I

Crystal structure of insulin regulated aminopeptidase in complex with ligand

PDB DOI: https://doi.org/10.2210/pdb4Z7I/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens, synthetic construct
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2015-04-07 Released: 2015-08-26
Deposition Author(s): Mpakali, A., Saridakis, E., Harlos, K., Zhao, Y., Stratikos, E.
Funding Organization(s): General Secretariat for Research & Technology, European Union

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.31 Å
R-Value Free: 0.270
R-Value Work: 0.211
R-Value Observed: 0.214

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: 217.29 kDa
Atom Count: 14,358
Modelled Residue Count: 1,726
Deposited Residue Count: 1,844
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucyl-cystinyl aminopeptidase	A, B	912	Homo sapiens	Mutation(s): 0 Gene Names: LNPEP, OTASE EC: 3.4.11.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIQ6 (Homo sapiens) Explore Q9UIQ6 Go to UniProtKB: Q9UIQ6
PHAROS: Q9UIQ6 GTEx: ENSG00000113441
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UIQ6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DG025 transition-state analogue enzyme inhibitor	C, D	10	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
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, I, J	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain H Focus chain I Focus chain J Interactions & Density Focus chain E Focus chain F Focus chain H Focus chain I Focus chain J
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	3		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] L [auth A] M [auth A] N [auth A] O [auth A] AA [auth B], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain S [auth B] MOL2 format, chain K [auth A] MOL2 format, chain S [auth B]	K [auth A], S [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain S [auth B] Interactions & Density Focus chain K [auth A] Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.31 Å
R-Value Free: 0.270
R-Value Work: 0.211
R-Value Observed: 0.214
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.52	α = 90
b = 256.35	β = 111.58
c = 73.06	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-08-26

Deposition Author(s):

Funding Organization	Location	Grant Number
General Secretariat for Research & Technology	Greece	ERC-14
European Union		FP7 BioStruct-X 283570

Revision History (Full details and data files)

Version 1.0: 2015-08-26
Type: Initial release
Version 1.1: 2015-09-16
Changes: Derived calculations
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

4Z7I

Crystal structure of insulin regulated aminopeptidase in complex with ligand

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2