3P4U

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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.185 
• R-Value Work: 0.150 
• R-Value Observed: 0.151 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

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

Macromolecules

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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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	E, F	N-acetyl-L-valyl-L-alpha-glutamyl-N-[(2S)-1-carboxy-3-hydroxypropan-2-yl]-L-isoleucinamide	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.185 
• R-Value Work: 0.150 
• R-Value Observed: 0.151 
• 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

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2011-09-28
  Type: Initial release
  
• Version 1.1: 2015-12-02
  Changes: Refinement description