7Q5W

The tandem SH2 domains of SYK with a bound TYROBP diphospho-ITAM peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The tandem SH2 domains of SYK

Bradshaw, W.J.Katis, V.L.Chen, Z.Bountra, C.von Delft, F.Gileadi, O.Brennan, P.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase SYKA [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD], E [auth EEE], F [auth FFF]265Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TYRO protein tyrosine kinase-binding proteinG [auth GGG], H [auth HHH], I [auth III], J [auth JJJ], K [auth KKK], L [auth LLL]20Homo sapiensMutation(s): 0 
Gene Names: TYROBPDAP12KARAP
UniProt & NIH Common Fund Data Resources
Find proteins for O43914 (Homo sapiens)
Explore O43914 
Go to UniProtKB:  O43914
PHAROS:  O43914
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P4G (Subject of Investigation/LOI)
Query on P4G

Download Ideal Coordinates CCD File 
V [auth EEE]1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
C8 H18 O3
RRQYJINTUHWNHW-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
R [auth CCC]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
M [auth AAA], O [auth BBB], Q [auth CCC], S [auth DDD], U [auth EEE], W [auth FFF]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
N [auth AAA], P [auth BBB], T [auth DDD]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
G [auth GGG], H [auth HHH], I [auth III], J [auth JJJ], K [auth KKK], L [auth LLL]L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.949α = 90
b = 131.928β = 90
c = 141.526γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United States5U54AG065187-03

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release