6GTT | pdb_00006gtt

Human STK10 bound to BIRB-796

PDB DOI: https://doi.org/10.2210/pdb6GTT/pdb

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

Deposited: 2018-06-19 Released: 2018-06-27
Deposition Author(s): Berger, B.T., Sorrell, F.J., von Delft, F., Bountra, C., Knapp, S., Edwards, A.M., Arrowsmith, C., Elkins, J.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.301 (Depositor), 0.300 (DCC)
R-Value Work:
0.240 (Depositor), 0.240 (DCC)
R-Value Observed:
0.244 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

STK10 bound to BIRB-796

Berger, B.T., Elkins, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 34.77 kDa
Atom Count: 2,250
Modeled Residue Count: 282
Deposited Residue Count: 302
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase 10	A	302	Homo sapiens	Mutation(s): 0 Gene Names: STK10, LOK EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O94804 (Homo sapiens) Explore O94804 Go to UniProtKB: O94804
PHAROS: O94804 GTEx: ENSG00000072786
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O94804
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B96 Query on B96 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1-(5-TERT-BUTYL-2-P-TOLYL-2H-PYRAZOL-3-YL)-3-[4-(2-MORPHOLIN-4-YL-ETHOXY)-NAPHTHALEN-1-YL]-UREA C₃₁ H₃₇ N₅ O₃ MVCOAUNKQVWQHZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
B96	BindingDB: 6GTT	Kd: min: 7.1, max: 12 (nM) from 2 assay(s)
B96	BindingDB: 6GTT	IC50: 1000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.301 (Depositor), 0.300 (DCC)
R-Value Work: 0.240 (Depositor), 0.240 (DCC)
R-Value Observed: 0.244 (Depositor)

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.667	α = 90
b = 100.667	β = 90
c = 145.786	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-06-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-06-27
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

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.