Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12777.61 
• Atom Count: 899 
• Residue Count: 106 
• Unique protein chains: 1

2OPY

Smac mimic bound to BIR3-XIAP

• DOI: 10.2210/pdb2OPY/pdb

• Classification: apoptosis activator
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21


• Deposited: 2007-01-30 Released: 2007-02-20 
• Deposition Author(s): Wist, A.D., Lu, G., Riedl, S.J., Shi, Y., McLendon, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.235 
• R-Value Work: 0.213 

Literature

Structure-activity based study of the Smac-binding pocket within the BIR3 domain of XIAP.

Wist, A.D., Gu, L., Riedl, S.J., Shi, Y., McLendon, G.L.

(2007) Bioorg.Med.Chem. 15: 2935-2943

• PubMed: 17336535 
• DOI: 10.1016/j.bmc.2007.02.010
• Primary Citation of Related Structures:  
  2OPZ


• PubMed Abstract: 
  

A small series of peptide mimics was designed and synthesized to contain a heterocyclic ring in place of the potentially labile N-terminal peptide bond of the tetrapeptide containing the Smac-XIAP-binding motif. Two Smac mimics were shown to bind to the BIR3 domain of XIAP with moderate affinity and one displayed increased activity in cells relative to the Smac peptides. The structures of BIR3-XIAP in complex with a Smac peptide and a peptide mimic were solved and analyzed to elucidate the structure-activity relationship surrounding the Smac-binding domain within BIR3-XIAP.

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Organizational Affiliation: 

Department of Chemistry, Princeton University, Princeton, NJ 08544, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Baculoviral IAP repeat-containing protein 4	A	106	Homo sapiens	Mutation(s): 0  Gene Names: XIAP (API3, BIRC4, IAP3) EC: 2.3.2.27
Find proteins for P98170 (Homo sapiens) Go to Gene View: XIAP Go to UniProtKB:  P98170

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO9	A	1-({2-[(1S)-1-AMINOETHYL]-1,3-OXAZOL-4-YL}CARBONYL)-L-PROLYL-L-TRYPTOPHAN C22 H25 N5 O5 FBRCDLGEWAXPMI-IWEFOYFVSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
CO9	Kd: 30000 nM (100) BINDINGDB
CO9	Kd: 30000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.235 
• R-Value Work: 0.213 
• Space Group: P 4₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 71.200	α = 90.00
b = 71.200	β = 90.00
c = 105.100	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASES	phasing
DENZO	data reduction
PHASER	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-01-30 
• Released Date: 2007-02-20 
• Deposition Author(s): Wist, A.D., Lu, G., Riedl, S.J., Shi, Y., McLendon, G.L.

Revision History 

• Version 1.0: 2007-02-20
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance