Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 20.38 kDa 
• Atom Count: 1494 
• Modelled Residue Count: 163 
• Deposited Residue Count: 176 
• Unique protein chains: 2

4J44

Crystal structure of XIAP-BIR2 domain with AIAV bound

• PDB DOI: 10.2210/pdb4J44/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-02-06 Released: 2013-09-25 
• Deposition Author(s): Lukacs, C.M., Janson, C.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.193 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Literature

The structure of XIAP BIR2: understanding the selectivity of the BIR domains.

Lukacs, C., Belunis, C., Crowther, R., Danho, W., Gao, L., Goggin, B., Janson, C.A., Li, S., Remiszewski, S., Schutt, A., Thakur, M.K., Singh, S.K., Swaminathan, S., Pandey, R., Tyagi, R., Gosu, R., Kamath, A.V., Kuglstatter, A.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1717-1725

• PubMed: 23999295 
• DOI: 10.1107/S0907444913016284
• Primary Citation of Related Structures:  
  4J3Y, 4J44, 4J45, 4J46, 4J47, 4J48


• PubMed Abstract: 
  

XIAP, a member of the inhibitor of apoptosis family of proteins, is a critical regulator of apoptosis. Inhibition of the BIR domain-caspase interaction is a promising approach towards treating cancer. Previous work has been directed towards inhibiting the BIR3-caspase-9 interaction, which blocks the intrinsic apoptotic pathway; selectively inhibiting the BIR2-caspase-3 interaction would also block the extrinsic pathway. The BIR2 domain of XIAP has successfully been crystallized; peptides and small-molecule inhibitors can be soaked into these crystals, which diffract to high resolution. Here, the BIR2 apo crystal structure and the structures of five BIR2-tetrapeptide complexes are described. The structural flexibility observed on comparing these structures, along with a comparison with XIAP BIR3, affords an understanding of the structural elements that drive selectivity between BIR2 and BIR3 and which can be used to design BIR2-selective inhibitors.

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Organizational Affiliation: 

Discovery Technologies, Hoffmann-La Roche, 340 Kingsland Street, Nutley, NJ 07110, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase XIAP	A, C	86	Homo sapiens	Mutation(s): 2  Gene Names: API3, BIRC4, IAP3, U32974, XIAP EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P98170 (Homo sapiens) Explore P98170  Go to UniProtKB:  P98170
PHAROS:  P98170

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDE (ALA-ILE-ALA-VAL)	B	4	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], E [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.193 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.889	α = 90
b = 74.889	β = 90
c = 109.022	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-06 
• Released Date: 2013-09-25 
Deposition Author(s): Lukacs, C.M., Janson, C.A.

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection, Refinement description