3P4U | pdb_00003p4u

Crystal structure of active caspase-6 in complex with Ac-VEID-CHO inhibitor

PDB DOI: https://doi.org/10.2210/pdb3P4U/pdb

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

Deposited: 2010-10-07 Released: 2011-09-28
Deposition Author(s): Mueller, I., Lamers, M.B.A.C., Ritchie, A.J., Dominguez, C., Munoz, I., Maillard, M., Kiselyov, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.185 (Depositor), 0.192 (DCC)
R-Value Work:
0.150 (Depositor), 0.157 (DCC)
R-Value Observed:
0.151 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structures of active and inhibitor-bound human Casp6

Mueller, I., Lamers, M.B.A.C., Ritchie, A.J., Dominguez, C., Munoz, I., Maillard, M., Kiselyov, A.

To be published.

Macromolecule Content

Total Structure Weight: 63.04 kDa
Atom Count: 4,526
Modeled Residue Count: 488
Deposited Residue Count: 540
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-6	A, C	157	Homo sapiens	Mutation(s): 0 Gene Names: CASP6, MCH2 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P55212
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-6	B, D	108	Homo sapiens	Mutation(s): 0 Gene Names: CASP6, MCH2 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P55212
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ac-VEID-CHO inhibitor	E, F	5	N/A	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAS Query on CAS	A, C	L-PEPTIDE LINKING	C₅ H₁₂ As N O₂ S		CYS

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000929 Query on PRD_000929	E, F	N-acetyl-L-valyl-L-alpha-glutamyl-N-[(2S)-1-carboxy-3-hydroxypropan-2-yl]-L-isoleucinamide	Peptide-like / Inhibitor		Interactions Focus chain E Focus chain F Interactions & Density Focus chain E Focus chain F

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.185 (Depositor), 0.192 (DCC)
R-Value Work: 0.150 (Depositor), 0.157 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.455	α = 90
b = 89.5	β = 111.73
c = 61.245	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-09-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-09-28
Type: Initial release
Version 1.1: 2015-12-02
Changes: Refinement description
Version 1.2: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary