4RMZ | pdb_00004rmz

Crystal Structure of IRAK-4

• PDB DOI: https://doi.org/10.2210/pdb4RMZ/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2014-10-22 Released: 2016-01-13 
• Deposition Author(s): Johnstone, S., Sudom, A., Liu, J., Walker, N.P., Wang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.296 (Depositor), 0.297 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Literature

Crystal structures of IRAK-4 kinase in complex with inhibitors: a serine/threonine kinase with tyrosine as a gatekeeper

Johnstone, S., Sudom, A., Liu, J., Walker, N.P., Wang, Z.

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: 70.23 kDa 
• Atom Count: 4,726 
• Modeled Residue Count: 571 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 receptor-associated kinase 4	A, B	307	Homo sapiens	Mutation(s): 0  Gene Names: IRAK4 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWZ3 (Homo sapiens) Explore Q9NWZ3  Go to UniProtKB:  Q9NWZ3
PHAROS:  Q9NWZ3 GTEx:  ENSG00000198001

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
T20	C [auth A], D [auth B]	3-nitro-N-[1-phenyl-5-(piperidin-1-ylmethyl)-1H-benzimidazol-2-yl]benzamide C26 H25 N5 O3 IEOZVBDPTHRYGK-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A, B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A, B	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.296 (Depositor), 0.297 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.73	α = 90
b = 116.81	β = 90
c = 140.92	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Johnstone, S., Sudom, A., Liu, J., Walker, N.P., Wang, Z.

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 1.1: 2016-03-23
  Changes: Non-polymer description
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary