4YJV | pdb_00004yjv

THE KINASE DOMAIN OF HUMAN SPLEEN TYROSINE (SYK) IN COMPLEX WITH GTC000250

PDB DOI: https://doi.org/10.2210/pdb4YJV/pdb

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

Deposited: 2015-03-03 Released: 2015-10-14
Deposition Author(s): Somers, D.O., Neu, M., Stuckey, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.222 (Depositor), 0.219 (DCC)
R-Value Work:
0.175 (Depositor), 0.172 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: other
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Ligand Structure Quality Assessment

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

Literature

THE KINASE DOMAIN OF HUMAN SPLEEN TYROSINE (SYK) IN COMPLEX WITH GTC000250

Somers, D.O., Neu, M., Stuckey, J.

To be published.

Macromolecule Content

Total Structure Weight: 33.26 kDa
Atom Count: 2,583
Modeled Residue Count: 265
Deposited Residue Count: 281
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase SYK	A	281	Homo sapiens	Mutation(s): 0 Gene Names: SYK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P43405 (Homo sapiens) Explore P43405 Go to UniProtKB: P43405
PHAROS: P43405 GTEx: ENSG00000165025
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43405
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4DT Query on 4DT 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]	3-[6-({4-[ethyl(1H-indazol-4-yl)amino]-5-fluoropyrimidin-2-yl}amino)-2,4-dihydro-1H-indazol-1-yl]propan-1-ol C₂₃ H₂₅ F N₈ O WTARZSVAAGFJEN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on PTR	A	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.222 (Depositor), 0.219 (DCC)
R-Value Work: 0.175 (Depositor), 0.172 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.46	α = 90
b = 86.94	β = 92.59
c = 40.43	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-10-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-10-14
Type: Initial release
Version 1.1: 2024-05-01
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.