4KMP | pdb_00004kmp

Structure of XIAP-BIR3 and inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4KMP/pdb

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


• Deposited: 2013-05-08 Released: 2014-05-14 
• Deposition Author(s): Li, X., Wang, J., Condon, S.M., Shi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Structure of XIAP-BIR3 and inhibitor

Li, X., Wang, J., Condon, S.M., Shi, Y.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 23.56 kDa 
• Atom Count: 1,783 
• Modeled Residue Count: 196 
• Deposited Residue Count: 196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase XIAP	A, B	98	Homo sapiens	Mutation(s): 0  Gene Names: XIAP, API3, BIRC4, IAP3 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 GTEx:  ENSG00000101966

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GT6	E [auth B]	(2S,2'S)-N,N'-[(6,6'-difluoro-1H,1'H-2,2'-biindole-3,3'-diyl)bis{methanediyl[(2R,4S)-4-hydroxypyrrolidine-2,1-diyl][(2S)-1-oxobutane-1,2-diyl]}]bis[2-(methylamino)propanamide] C42 H56 F2 N8 O6 PKWRMUKBEYJEIX-DXXQBUJASA-N
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GT6	BindingDB:  4KMP	Kd: 50 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.016	α = 77.97
b = 33.281	β = 70.54
c = 48.002	γ = 61.28

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-14 
Deposition Author(s): Li, X., Wang, J., Condon, S.M., Shi, Y.

Revision History  

• Version 1.0: 2014-05-14
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description