7Q7C

Room temperature structure of the human Serine/Threonine Kinase 17B (STK17B/DRAK2) in complex with ADP at atmospheric pressure

PDB DOI: https://doi.org/10.2210/pdb7Q7C/pdb

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

Deposited: 2021-11-09 Released: 2022-11-16
Deposition Author(s): Lieske, J., Guenther, S., Saouane, S., Meents, A.
Funding Organization(s): German Federal Ministry for Education and Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.238
R-Value Work: 0.207
R-Value Observed: 0.210

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Room temperature structure of the human Serine/Threonine Kinase 17B (STK17B/DRAK2) in complex with ADP at atmospheric pressure

Lieske, J., Saouane, S., Guenther, S., Meyer, J., Pakendorf, T., Reime, B., Burkhardt, A., Crosas, E., Hakanpaeae, J., Stachnik, K., Sieg, J., Rarey, M., Abdellatif, M.H., Gabdulkhakov, A.G., Selikhanov, G.K., Chapman, H.N., Meents, A.

To be published.

Macromolecule Content

Total Structure Weight: 37.78 kDa
Atom Count: 2,231
Modelled Residue Count: 272
Deposited Residue Count: 327
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 17B	A	327	Homo sapiens	Mutation(s): 0 Gene Names: STK17B, DRAK2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O94768 (Homo sapiens) Explore O94768 Go to UniProtKB: O94768
PHAROS: O94768 GTEx: ENSG00000081320
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O94768
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.238
R-Value Work: 0.207
R-Value Observed: 0.210
Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.44	α = 90
b = 84.44	β = 90
c = 116.61	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-16

Deposition Author(s):

Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	031B0405A

Revision History (Full details and data files)

Version 1.0: 2022-11-16
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, 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 R01GM133198.