6VZH

Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to LDSM311

PDB DOI: https://doi.org/10.2210/pdb6VZH/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-02-28 Released: 2020-03-11
Deposition Author(s): dos Reis, C.V., Dutra, L.A., Gama, F., Ferreira, M., Mascarello, A., Azevedo, H., Guimaraes, C., Massirer, K.B., Arruda, P., Edwards, A.M., Counago, R.M., Structural Genomics Consortium (SGC)
Funding Organization(s): Sao Paulo Research Foundation (FAPESP), Brazilian National Council for Scientific and Technological Development (CNPq)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.251
R-Value Work: 0.216
R-Value Observed: 0.217

wwPDB Validation 3D Report Full Report

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

Literature

Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to LDSM311

dos Reis, C.V., Dutra, L.A., Gama, F., Ferreira, M., Mascarello, A., Azevedo, H., Guimaraes, C.R.W., Massirer, K.B., Arruda, P., Edwards, A.M., Counago, R.M.

To be published.

Macromolecule Content

Total Structure Weight: 166.2 kDa
Atom Count: 9,695
Modelled Residue Count: 1,244
Deposited Residue Count: 1,456
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 VRK1	A, B, C, D	364	Homo sapiens	Mutation(s): 11 Gene Names: VRK1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99986 (Homo sapiens) Explore Q99986 Go to UniProtKB: Q99986
PHAROS: Q99986 GTEx: ENSG00000100749
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99986
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RYA (Subject of Investigation/LOI) Query on RYA Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain P [auth D] MOL2 format, chain J [auth B] MOL2 format, chain P [auth D]	J [auth B], P [auth D]	(7~{R})-2-[[3,5-bis(fluoranyl)-4-oxidanyl-phenyl]amino]-5,7-dimethyl-8-prop-2-ynyl-7~{H}-pteridin-6-one C₁₇ H₁₅ F₂ N₅ O₂ DYKLQWQETZOVEI-SECBINFHSA-N		Interactions Focus chain J [auth B] Focus chain P [auth D] Interactions & Density Focus chain J [auth B] Focus chain P [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D]	E [auth A] F [auth A] G [auth B] H [auth B] I [auth B] E [auth A], F [auth A], G [auth B], H [auth B], I [auth B], K [auth C], L [auth C], M [auth D], N [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain O [auth D] MOL2 format, chain O [auth D]	O [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain O [auth D] Interactions & Density Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.251
R-Value Work: 0.216
R-Value Observed: 0.217
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.158	α = 90
b = 95.641	β = 90
c = 192.593	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2020-03-11

Deposition Author(s):

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	13/50724-5
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	465651/2014-3
Sao Paulo Research Foundation (FAPESP)	Brazil	2014/50897-0

Revision History (Full details and data files)

Version 1.0: 2020-03-11
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

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Help and Resources

6VZH

Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to LDSM311

Structure of Human Vaccinia-related Kinase 1 (VRK1) Bound to LDSM311

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)