2OPZ | pdb_00002opz

AVPF bound to BIR3-XIAP

• PDB DOI: https://doi.org/10.2210/pdb2OPZ/pdb

• Classification: apoptosis inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-01-30 Released: 2007-02-20 
• Deposition Author(s): Wist, A.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.277 (Depositor) 
• R-Value Work: 
  0.231 (Depositor) 
• R-Value Observed: 
  0.231 (Depositor) 

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: https://doi.org/10.1016/j.bmc.2007.02.010
• Primary Citation Related Structures: 
  2OPY, 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]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content 

• Total Structure Weight: 52.41 kDa 
• Atom Count: 3,680 
• Modeled Residue Count: 452 
• Deposited Residue Count: 452 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Baculoviral IAP repeat-containing protein 4	A, B, C, D	109	Homo sapiens	Mutation(s): 0  Gene Names: BIRC4, API3, IAP3, XIAP EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P98170 (Homo sapiens) Explore P98170  Go to UniProtKB:  P98170
PHAROS:  P98170 GTEx:  ENSG00000101966

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AVPF (Smac homologue, N-terminal tetrapeptide)	E, F, G, H	4	N/A	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.277 (Depositor) 
• R-Value Work:  0.231 (Depositor) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.367	α = 90
b = 170.367	β = 90
c = 170.367	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-20 
Deposition Author(s): Wist, A.D.

Revision History  

• Version 1.0: 2007-02-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-09-04
  Changes: Data collection
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Structure summary