3ZON | pdb_00003zon

Human TYK2 pseudokinase domain bound to a kinase inhibitor

PDB DOI: https://doi.org/10.2210/pdb3ZON/pdb

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

Deposited: 2013-02-22 Released: 2013-04-10
Deposition Author(s): Elkins, J.M., Wang, J., Krojer, T., Savitsky, P., Chalk, R., Daga, N., Salah, E., Berridge, G., Picaud, S., von Delft, F., Bountra, C., Edwards, A., Knapp, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.268 (Depositor), 0.265 (DCC)
R-Value Work:
0.214 (Depositor), 0.220 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Human Tyk2 Pseudokinase Domain Bound to a Kinase Inhibitor

Elkins, J.M., Wang, J., Krojer, T., Savitsky, P., Chalk, R., Daga, N., Salah, E., Berridge, G., Picaud, S., von Delft, F., Bountra, C., Edwards, A., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 37.67 kDa
Atom Count: 2,185
Modeled Residue Count: 261
Deposited Residue Count: 335
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NON-RECEPTOR TYROSINE-PROTEIN KINASE TYK2	A	335	Homo sapiens	Mutation(s): 0 EC: 2.7.11.1 (PDB Primary Data), 2.7.10.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P29597 (Homo sapiens) Explore P29597 Go to UniProtKB: P29597
PHAROS: P29597 GTEx: ENSG00000105397
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29597
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IK1 Query on IK1 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	5-PHENYL-2-UREIDOTHIOPHENE-3-CARBOXAMIDE C₁₂ H₁₁ N₃ O₂ S PSVUSJKZJQMCSP-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.268 (Depositor), 0.265 (DCC)
R-Value Work: 0.214 (Depositor), 0.220 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.81	α = 90
b = 83.72	β = 90
c = 91.22	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-04-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-04-10
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description