6VG3 | pdb_00006vg3

Structure of unliganded, inactive PTK7 kinase domain

PDB DOI: https://doi.org/10.2210/pdb6VG3/pdb

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

Deposited: 2020-01-07 Released: 2020-05-27
Deposition Author(s): Malhotra, K., Stayrook, S.E., Sheetz, J., Lemmon, M.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.244 (Depositor), 0.249 (DCC)
R-Value Work:
0.189 (Depositor), 0.194 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6VG3

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

Literature

Structural insights into receptor tyrosine kinase pseudokinase function

Sheetz, J.B., Mathea, S., Karvonen, H., Malhotra, K., Chaterjee, D., Perttila, R., Niininen, W., Stayrook, S.E., Radhakrishnan, R., Ungureanu, D., Knapp, S., Lemmon, M.A.

(2020) Mol Cell

Macromolecule Content

Total Structure Weight: 99.85 kDa
Atom Count: 7,161
Modeled Residue Count: 821
Deposited Residue Count: 888
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inactive tyrosine-protein kinase 7	A, B, C	296	Homo sapiens	Mutation(s): 0 Gene Names: PTK7, CCK4
UniProt & NIH Common Fund Data Resources
Find proteins for Q13308 (Homo sapiens) Explore Q13308 Go to UniProtKB: Q13308
PHAROS: Q13308 GTEx: ENSG00000112655
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13308
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.244 (Depositor), 0.249 (DCC)
R-Value Work: 0.189 (Depositor), 0.194 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.628	α = 90
b = 119.918	β = 90
c = 166.516	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
PHASER	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-05-27

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM122485

Revision History (Full details and data files)

Version 1.0: 2020-05-27
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

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.