2P82

Cysteine protease ATG4A

PDB DOI: https://doi.org/10.2210/pdb2P82/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-03-21 Released: 2007-04-10
Deposition Author(s): Walker, J.R., Davis, T., Mujib, S., Butler-Cole, C., Finerty Jr., P.J., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.213 (Depositor), 0.210 (DCC)
R-Value Work:
0.175 (Depositor), 0.170 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Human cysteine protease ATG4A

Walker, J.R., Davis, T., Mujib, S., Butler-Cole, C., Finerty Jr., P.J., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

To be published.

Macromolecule Content

Total Structure Weight: 163.26 kDa
Atom Count: 10,944
Modelled Residue Count: 1,232
Deposited Residue Count: 1,420
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine protease ATG4A	A, B, C, D	355	Homo sapiens	Mutation(s): 0 Gene Names: ATG4A, APG4A, AUTL2 EC: 3.4.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WYN0 (Homo sapiens) Explore Q8WYN0 Go to UniProtKB: Q8WYN0
PHAROS: Q8WYN0 GTEx: ENSG00000101844
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8WYN0
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth B] E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth C], M [auth C], N [auth C], O [auth C], Q [auth D], R [auth D], S [auth D], T [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain P [auth D] MOL2 format, chain P [auth D] mmCIF format, chain P [auth D]	P [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain P [auth D] Interactions & Density Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.213 (Depositor), 0.210 (DCC)
R-Value Work: 0.175 (Depositor), 0.170 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.408	α = 90
b = 94.408	β = 90
c = 337.339	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-04-10

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-04-10
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description