7SIY | pdb_00007siy

cCBL TKB domain in complex with pZAP70 peptide

PDB DOI: https://doi.org/10.2210/pdb7SIY/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-10-15 Released: 2022-11-09
Deposition Author(s): Murray, J.M., Yu, C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free:
0.221 (Depositor), 0.220 (DCC)
R-Value Work:
0.208 (Depositor), 0.200 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

cCBL TKB domain in complex with pZAP70 peptide

Murray, J.M., Yu, C.

To be published.

Macromolecule Content

Total Structure Weight: 36.07 kDa
Atom Count: 2,912
Modelled Residue Count: 311
Deposited Residue Count: 311
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase CBL	A	304	Homo sapiens	Mutation(s): 0 Gene Names: CBL, CBL2, RNF55 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for P22681 (Homo sapiens) Explore P22681 Go to UniProtKB: P22681
PHAROS: P22681 GTEx: ENSG00000110395
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22681
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from Tyrosine-protein kinase ZAP-70	B [auth Z]	7	Homo sapiens	Mutation(s): 2 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P43403 (Homo sapiens) Explore P43403 Go to UniProtKB: P43403
PHAROS: P43403 GTEx: ENSG00000115085
Entity Groups
UniProt Group	P43403
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.221 (Depositor), 0.220 (DCC)
R-Value Work: 0.208 (Depositor), 0.200 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.519	α = 90
b = 123.519	β = 90
c = 56.598	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
DIMPLE	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-11-09
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection
Version 1.3: 2024-10-23
Changes: Structure summary

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.