6Z59 | pdb_00006z59

Crystal structure of haspin (GSG2) in complex with macrocycle ODS2003816

PDB DOI: https://doi.org/10.2210/pdb6Z59/pdb

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

Deposited: 2020-05-26 Released: 2020-06-03
Deposition Author(s): Chaikuad, A., Benderitter, P., Hoflack, J., Denis, A., Knapp, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.240 (Depositor), 0.235 (DCC)
R-Value Work:
0.199 (Depositor), 0.202 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of haspin (GSG2) in complex with macrocycle ODS2003816

Chaikuad, A., Benderitter, P., Hoflack, J., Denis, A., Knapp, S., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 41.06 kDa
Atom Count: 2,874
Modeled Residue Count: 328
Deposited Residue Count: 357
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase haspin	A	357	Homo sapiens	Mutation(s): 0 Gene Names: HASPIN, GSG2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TF76 (Homo sapiens) Explore Q8TF76 Go to UniProtKB: Q8TF76
PHAROS: Q8TF76 GTEx: ENSG00000177602
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TF76
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Q98 (Subject of Investigation/LOI) Query on Q98 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]	11-oxa-8,14,18,19,22-pentazatetracyclo[13.5.2.12,6.018,21]tricosa-1(21),2,4,6(23),15(22),16,19-heptaen-7-one C₁₇ H₁₇ N₅ O₂ SOQJGMPMKVQEAL-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.240 (Depositor), 0.235 (DCC)
R-Value Work: 0.199 (Depositor), 0.202 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.159	α = 90
b = 78.29	β = 90
c = 86.52	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-06-03

Deposition Author(s):

Benderitter, P.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2020-06-03
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.