7Q5U

The tandem SH2 domains of SYK with a bound CD3G diphospho-ITAM peptide

PDB DOI: https://doi.org/10.2210/pdb7Q5U/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: 2.40 Å
R-Value Free: 0.259
R-Value Work: 0.216

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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.

Macromolecule Content

Total Structure Weight: 196.17 kDa
Atom Count: 14,063
Modelled Residue Count: 1,657
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
T-cell surface glycoprotein CD3 gamma chain	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 P09693 (Homo sapiens) Explore P09693 Go to UniProtKB: P09693
PHAROS: P09693 GTEx: ENSG00000160654
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09693
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P4G Query on P4G Download Ideal Coordinates CCD File SDF format, chain P [auth AAA] SDF format, chain V [auth EEE] MOL2 format, chain P [auth AAA] MOL2 format, chain V [auth EEE]	P [auth AAA], V [auth EEE]	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE C₈ H₁₈ O₃ RRQYJINTUHWNHW-UHFFFAOYSA-N		Interactions Focus chain P [auth AAA] Focus chain V [auth EEE] Interactions & Density Focus chain P [auth AAA] Focus chain V [auth EEE]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain O [auth AAA] SDF format, chain Q [auth BBB] SDF format, chain U [auth EEE] SDF format, chain W [auth FFF] MOL2 format, chain O [auth AAA] MOL2 format, chain Q [auth BBB] MOL2 format, chain U [auth EEE] MOL2 format, chain W [auth FFF]	O [auth AAA], Q [auth BBB], U [auth EEE], W [auth FFF]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain O [auth AAA] Focus chain Q [auth BBB] Focus chain U [auth EEE] Focus chain W [auth FFF] Interactions & Density Focus chain O [auth AAA] Focus chain Q [auth BBB] Focus chain U [auth EEE] Focus chain W [auth FFF]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain M [auth AAA] SDF format, chain N [auth AAA] SDF format, chain R [auth CCC] SDF format, chain S [auth CCC] SDF format, chain T [auth DDD] MOL2 format, chain M [auth AAA] MOL2 format, chain N [auth AAA] MOL2 format, chain R [auth CCC] MOL2 format, chain S [auth CCC] MOL2 format, chain T [auth DDD]	M [auth AAA], N [auth AAA], R [auth CCC], S [auth CCC], T [auth DDD]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain M [auth AAA] Focus chain N [auth AAA] Focus chain R [auth CCC] Focus chain S [auth CCC] Focus chain T [auth DDD] Interactions & Density Focus chain M [auth AAA] Focus chain N [auth AAA] Focus chain R [auth CCC] Focus chain S [auth CCC] Focus chain T [auth DDD]

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