8EEC | pdb_00008eec

Crystal structure of HPK1 citron-homology domain

PDB DOI: https://doi.org/10.2210/pdb8EEC/pdb

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

Deposited: 2022-09-06 Released: 2024-03-27
Deposition Author(s): Wu, P., Lehoux, I., Wang, W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.257 (Depositor), 0.260 (DCC)
R-Value Work:
0.208 (Depositor), 0.213 (DCC)
R-Value Observed:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8EEC

This is version 1.1 of the entry. See complete history.

Literature

HPK1 citron homology domain regulates phosphorylation of SLP76 and modulates kinase domain interaction dynamics

Chitre, A.S., Wu, P., Walters, B.T., Wang, X., Bouyssou, A., Du, X., Lehoux, I., Fong, R., Arata, A., Chan, J., Wang, D., Franke, Y., Grogan, J.L., Mellman, I., Comps-Agrar, L., Wang, W.

(2024) Nat Commun 15: 3725

DOI: https://doi.org/10.1038/s41467-024-48014-9

Macromolecule Content

Total Structure Weight: 37.97 kDa
Atom Count: 2,553
Modeled Residue Count: 317
Deposited Residue Count: 343
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Mitogen-activated protein kinase kinase kinase kinase 1	A	343	Homo sapiens	Mutation(s): 0 Gene Names: MAP4K1, HPK1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92918 (Homo sapiens) Explore Q92918 Go to UniProtKB: Q92918
PHAROS: Q92918 GTEx: ENSG00000104814
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92918
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.257 (Depositor), 0.260 (DCC)
R-Value Work: 0.208 (Depositor), 0.213 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.667	α = 90
b = 81.667	β = 90
c = 140.535	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
AutoSol	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-03-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-03-27
Type: Initial release
Version 1.1: 2024-10-09
Changes: Database references, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.