4AZ3

crystal structure of cathepsin a, complexed with 15a

PDB DOI: https://doi.org/10.2210/pdb4AZ3/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2012-06-22 Released: 2012-09-26
Deposition Author(s): Ruf, S., Buning, C., Schreuder, H., Horstick, G., Linz, W., Olpp, T., Pernerstorfer, J., Hiss, K., Kroll, K., Kannt, A., Kohlmann, M., Linz, D., Huebschle, T., Ruetten, H., Wirth, K., Schmidt, T., Sadowski, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.215
R-Value Work: 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: 53.63 kDa
Atom Count: 3,854
Modelled Residue Count: 414
Deposited Residue Count: 455
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOSOMAL PROTECTIVE PROTEIN 32 KDA CHAIN	A	300	Homo sapiens	Mutation(s): 0 EC: 3.4.16.5
UniProt & NIH Common Fund Data Resources
Find proteins for P10619 (Homo sapiens) Explore P10619 Go to UniProtKB: P10619
PHAROS: P10619 GTEx: ENSG00000064601
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10619
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOSOMAL PROTECTIVE PROTEIN 20 KDA CHAIN	B	155	Homo sapiens	Mutation(s): 0 EC: 3.4.16.5
UniProt & NIH Common Fund Data Resources
Find proteins for P10619 (Homo sapiens) Explore P10619 Go to UniProtKB: P10619
PHAROS: P10619 GTEx: ENSG00000064601
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10619
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	C, D	2		N-Glycosylation	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
S35 Query on S35 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	(3S)-3-({[1-(2-fluorophenyl)-5-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-1H-pyrazol-3-yl]carbonyl}amino)-3-(2-methylphenyl)propanoic acid C₂₆ H₃₀ F N₃ O₅ PUJVTKSRQZHCAT-UGKGYDQZSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B]	F [auth A], G [auth A], H [auth A], I [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
S35	BindingDB: 4AZ3	IC50: 5 (nM) from 1 assay(s)
	PDBBind: 4AZ3	IC50: 5 (nM) from 1 assay(s)
	Binding MOAD: 4AZ3	IC50: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.215
R-Value Work: 0.188
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.59	α = 90
b = 102.8	β = 101.87
c = 48.39	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-09-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-09-26
Type: Initial release
Version 1.1: 2019-04-03
Changes: Data collection, Derived calculations, Experimental preparation, Other
Version 1.2: 2019-05-08
Changes: Data collection, Experimental preparation
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary