3OD5 | pdb_00003od5

Crystal structure of active caspase-6 bound with Ac-VEID-CHO

PDB DOI: https://doi.org/10.2210/pdb3OD5/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-08-11 Released: 2010-10-27
Deposition Author(s): Wang, X.-J., Liu, X., Wang, K.-T., Cao, Q., Su, X.-D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.189 (Depositor), 0.187 (DCC)
R-Value Work:
0.155 (Depositor), 0.152 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structures of human caspase 6 reveal a new mechanism for intramolecular cleavage self-activation

Wang, X.-J., Cao, Q., Liu, X., Wang, K.-T., Mi, W., Zhang, Y., Li, L.-F., Leblanc, A.C., Su, X.-D.

(2010) EMBO Rep 11: 841-847

PubMed: 20890311 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/embor.2010.141
Primary Citation Related Structures:
3NR2, 3OD5

PubMed Abstract:
Dimeric effectors caspase 3 and caspase 7 are activated by initiator caspase processing. In this study, we report the crystal structures of effector caspase 6 (CASP6) zymogen and N-Acetyl-Val-Glu-Ile-Asp-al-inhibited CASP6. Both of these forms of CASP6 have a dimeric structure, and in CASP6 zymogen the intersubunit cleavage site (190)TEVD(193) is well structured and inserts into the active site. This positions residue Asp 193 to be easily attacked by the catalytic residue Cys 163. We demonstrate biochemically that intramolecular cleavage at Asp 193 is a prerequisite for CASP6 self-activation and that this activation mechanism is dependent on the length of the L2 loop. Our results indicate that CASP6 can be activated and regulated through intramolecular self-cleavage.

Organizational Affiliation

National Laboratory of Protein Engineering & Plant Genetic Engineering, Peking University, Haidian District, Beijing, People's Republic of China.

Macromolecule Content

Total Structure Weight: 66.17 kDa
Atom Count: 4,688
Modeled Residue Count: 490
Deposited Residue Count: 566
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-6	A, C [auth B]	278	Homo sapiens	Mutation(s): 0 EC: 3.4.22.59
UniProt & NIH Common Fund Data Resources
Find proteins for P55212 (Homo sapiens) Explore P55212 Go to UniProtKB: P55212
PHAROS: P55212 GTEx: ENSG00000138794
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P55212
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide aldehyde inhibitor AC-VEID-CHO	B [auth C], D	5	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAC Query on CAC 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 J [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A]	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 B]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		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 B] 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 B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ASA Query on ASA	B [auth C], D	L-PEPTIDE LINKING	C₄ H₇ N O₃		ASP

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000976 Query on PRD_000976	B [auth C], D	N-acetyl-L-valyl-L-alpha-glutamyl-N-[(2S)-1-carboxy-3-oxopropan-2-yl]-L-isoleucinamide	Polypeptide / Inhibitor		Interactions Focus chain B [auth C] Focus chain D Interactions & Density Focus chain B [auth C] Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.189 (Depositor), 0.187 (DCC)
R-Value Work: 0.155 (Depositor), 0.152 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.464	α = 90
b = 89.589	β = 111.67
c = 61.145	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-10-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-10-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-12-12
Changes: Other
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-12-06
Changes: Data collection
Version 1.5: 2024-11-13
Changes: Structure summary