2XIK

Structure of Human YSK1 (Yeast Sps1-Ste20-related Kinase 1)

PDB DOI: https://doi.org/10.2210/pdb2XIK/pdb

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

Deposited: 2010-06-30 Released: 2010-07-14
Deposition Author(s): Muniz, J.R.C., Rellos, P., Ugochukwu, E., Vollmar, M., Allerston, C., Chaikuad, A., Savitsky, P., Berridge, G., Brenner, B., Elkins, J.M., Daga, N., Gileadi, O., Mahajan, P., Shrestha, B., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.233 (Depositor), 0.248 (DCC)
R-Value Work:
0.188 (Depositor), 0.201 (DCC)
R-Value Observed:
0.191 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of Human Ysk1 (Yeast Sps1-Ste20-Related Kinase 1)

Muniz, J.R.C., Rellos, P., Vollmar, M., Allerston, C., Chaikuad, A., Savitsky, P., Berridge, G., Brenner, B., Elkins, J.M., Daga, N., Gileadi, O., Mahajan, P., Shrestha, B., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 34.19 kDa
Atom Count: 2,474
Modelled Residue Count: 289
Deposited Residue Count: 294
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 25	A	294	Homo sapiens	Mutation(s): 0 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O00506 (Homo sapiens) Explore O00506 Go to UniProtKB: O00506
PHAROS: O00506 GTEx: ENSG00000115694
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00506
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
J60 Query on J60 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]	5-[(E)-(5-CHLORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-N-[2-(DIETHYLAMINO)ETHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE C₂₂ H₂₇ Cl N₄ O₂ XPLJEFSRINKZLC-ATVHPVEESA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO Query on TPO	A	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.233 (Depositor), 0.248 (DCC)
R-Value Work: 0.188 (Depositor), 0.201 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.08	α = 90
b = 48.56	β = 113.78
c = 67.57	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-07-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-07-14
Type: Initial release
Version 1.1: 2012-12-05
Changes: Database references, Source and taxonomy, Structure summary, Version format compliance
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Other, Structure summary