2X7G

Structure of human serine-arginine-rich protein-specific kinase 2 (SRPK2) bound to purvalanol B

PDB DOI: https://doi.org/10.2210/pdb2X7G/pdb

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

Deposited: 2010-02-26 Released: 2010-04-14
Deposition Author(s): Pike, A.C.W., Savitsky, P., Fedorov, O., Krojer, T., Ugochukwu, E., von Delft, F., Gileadi, O., Edwards, A., Arrowsmith, C.H., Weigelt, J., Bountra, C., Knapp, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.249
R-Value Work: 0.183
R-Value Observed: 0.186

Starting Model: experimental
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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 Serine-Arginine-Rich Protein- Specific Kinase 2 (Srpk2) Bound to Purvalanol B

Pike, A.C.W., Savitsky, P., Fedorov, O., Krojer, T., Ugochukwu, E., von Delft, F., Gileadi, O., Edwards, A., Arrowsmith, C.H., Weigelt, J., Bountra, C., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 45.84 kDa
Atom Count: 2,969
Modelled Residue Count: 344
Deposited Residue Count: 389
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UNCHARACTERIZED PROTEIN SRPK2	A	389	Homo sapiens	Mutation(s): 0 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P78362 (Homo sapiens) Explore P78362 Go to UniProtKB: P78362
PHAROS: P78362 GTEx: ENSG00000135250
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P78362
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PVB Query on PVB 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]	PURVALANOL B C₂₀ H₂₅ Cl N₆ O₃ ZKDXRFMOHZVXSG-HNNXBMFYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions 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] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density 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] Focus chain H [auth A] Focus chain I [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	K [auth A] L [auth A] M [auth A] N [auth A] O [auth A] K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.249
R-Value Work: 0.183
R-Value Observed: 0.186
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.31	α = 90
b = 110.31	β = 90
c = 90.59	γ = 120

Software Package:

Software Name	Purpose
REFMAC	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: 2010-04-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-04-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description