7Q5T

The tandem SH2 domains of SYK with a bound FCER1G diphospho-ITAM peptide

PDB DOI: https://doi.org/10.2210/pdb7Q5T/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-11-04 Released: 2021-11-24
Deposition Author(s): Bradshaw, W.J., Katis, V.L., Chen, Z., Bountra, C., von Delft, F., Gileadi, O., Brennan, P.E.
Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.255
R-Value Work: 0.207

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The mechanism of allosteric activation of SYK kinase derived from multiple phospho-ITAM-bound structures

Bradshaw, W.J., Harris, G., Gileadi, O., Katis, V.L.

(2024) Structure

DOI: https://doi.org/10.1016/j.str.2024.09.024

Macromolecule Content

Total Structure Weight: 195.55 kDa
Atom Count: 13,506
Modelled Residue Count: 1,630
Deposited Residue Count: 1,710
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase SYK	A [auth AAA] B [auth BBB] C [auth CCC] D [auth DDD] E [auth EEE] A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD], E [auth EEE], F [auth FFF]	265	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43405
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity immunoglobulin epsilon receptor subunit gamma	G [auth GGG] H [auth HHH] I [auth III] J [auth JJJ] K [auth KKK] G [auth GGG], H [auth HHH], I [auth III], J [auth JJJ], K [auth KKK], L [auth LLL]	20	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P30273 (Homo sapiens) Explore P30273 Go to UniProtKB: P30273
PHAROS: P30273 GTEx: ENSG00000158869
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30273
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain R [auth BBB] SDF format, chain Z [auth EEE] MOL2 format, chain R [auth BBB] MOL2 format, chain Z [auth EEE] mmCIF format, chain R [auth BBB] mmCIF format, chain Z [auth EEE]	R [auth BBB], Z [auth EEE]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain R [auth BBB] Focus chain Z [auth EEE] Interactions & Density Focus chain R [auth BBB] Focus chain Z [auth EEE]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain M [auth AAA] SDF format, chain N [auth AAA] SDF format, chain P [auth BBB] SDF format, chain Q [auth BBB] SDF format, chain S [auth CCC] SDF format, chain T [auth CCC] SDF format, chain W [auth DDD] SDF format, chain X [auth DDD] SDF format, chain Y [auth DDD] MOL2 format, chain M [auth AAA] MOL2 format, chain N [auth AAA] MOL2 format, chain P [auth BBB] MOL2 format, chain Q [auth BBB] MOL2 format, chain S [auth CCC] MOL2 format, chain T [auth CCC] MOL2 format, chain W [auth DDD] MOL2 format, chain X [auth DDD] MOL2 format, chain Y [auth DDD] mmCIF format, chain M [auth AAA] mmCIF format, chain N [auth AAA] mmCIF format, chain P [auth BBB] mmCIF format, chain Q [auth BBB] mmCIF format, chain S [auth CCC] mmCIF format, chain T [auth CCC] mmCIF format, chain W [auth DDD] mmCIF format, chain X [auth DDD] mmCIF format, chain Y [auth DDD]	M [auth AAA] N [auth AAA] P [auth BBB] Q [auth BBB] S [auth CCC] M [auth AAA], N [auth AAA], P [auth BBB], Q [auth BBB], S [auth CCC], T [auth CCC], W [auth DDD], X [auth DDD], Y [auth DDD]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain M [auth AAA] Focus chain N [auth AAA] Focus chain P [auth BBB] Focus chain Q [auth BBB] Focus chain S [auth CCC] Focus chain T [auth CCC] Focus chain W [auth DDD] Focus chain X [auth DDD] Focus chain Y [auth DDD] Interactions & Density Focus chain M [auth AAA] Focus chain N [auth AAA] Focus chain P [auth BBB] Focus chain Q [auth BBB] Focus chain S [auth CCC] Focus chain T [auth CCC] Focus chain W [auth DDD] Focus chain X [auth DDD] Focus chain Y [auth DDD]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain O [auth AAA] SDF format, chain U [auth CCC] SDF format, chain V [auth CCC] MOL2 format, chain O [auth AAA] MOL2 format, chain U [auth CCC] MOL2 format, chain V [auth CCC] mmCIF format, chain O [auth AAA] mmCIF format, chain U [auth CCC] mmCIF format, chain V [auth CCC]	O [auth AAA], U [auth CCC], V [auth CCC]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain O [auth AAA] Focus chain U [auth CCC] Focus chain V [auth CCC] Interactions & Density Focus chain O [auth AAA] Focus chain U [auth CCC] Focus chain V [auth CCC]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on PTR	G [auth GGG] H [auth HHH] I [auth III] J [auth JJJ] K [auth KKK] G [auth GGG], H [auth HHH], I [auth III], J [auth JJJ], K [auth KKK], L [auth LLL]	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.255
R-Value Work: 0.207
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.136	α = 90
b = 88.035	β = 113.575
c = 158.486	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-11-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	5U54AG065187-03

Revision History (Full details and data files)

Version 1.0: 2021-11-24
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Derived calculations, Refinement description
Version 1.2: 2024-10-30
Changes: Database references, Structure summary

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Help and Resources

7Q5T

The tandem SH2 domains of SYK with a bound FCER1G diphospho-ITAM peptide

The mechanism of allosteric activation of SYK kinase derived from multiple phospho-ITAM-bound structures

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2