Macromolecule Content

Total Structure Weight: 70.23 kDa
Atom Count: 4,726
Modelled Residue Count: 571
Deposited Residue Count: 614
Unique protein chains: 1

4RMZ

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.296
R-Value Work: 0.236
R-Value Observed: 0.239

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NWZ3
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T20 Query on T20 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	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		Ligand Interaction

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A, B	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER
TPO Query on 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
R-Value Work: 0.236
R-Value Observed: 0.239
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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-01-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-01-13
Type: Initial release
Version 1.1: 2016-03-23
Changes: Non-polymer description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.