2QKR | pdb_00002qkr

Cryptosporidium parvum cyclin-dependent kinase cgd5_2510 with indirubin 3'-monoxime bound

PDB DOI: https://doi.org/10.2210/pdb2QKR/pdb

Classification: TRANSFERASE
Organism(s): Cryptosporidium parvum Iowa II
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-07-11 Released: 2007-09-04
Deposition Author(s): Wernimont, A.K., Dong, A., Lew, J., Lin, Y.H., Hassanali, A., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Sundstrom, M., Bochkarev, A., Hui, R., Artz, J.D., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.300 (Depositor), 0.317 (DCC)
R-Value Work:
0.247 (Depositor), 0.276 (DCC)
R-Value Observed:
0.249 (Depositor)

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

Cryptosporidium parvum cyclin-dependent kinase cgd5_2510 with indirubin 3'-monoxime bound.

Wernimont, A.K., Dong, A., Lew, J., Lin, Y.H., Hassanali, A., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Sundstrom, M., Bochkarev, A., Hui, R., Artz, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 36.37 kDa
Atom Count: 2,222
Modeled Residue Count: 273
Deposited Residue Count: 313
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cdc2-like CDK2/CDC28 like protein kinase	A	313	Cryptosporidium parvum Iowa II	Mutation(s): 0 Gene Names: cgd5_2510 EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (UniProt)
UniProt
Find proteins for Q5CRJ8 (Cryptosporidium parvum (strain Iowa II)) Explore Q5CRJ8 Go to UniProtKB: Q5CRJ8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5CRJ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IXM Query on IXM 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]	(Z)-1H,1'H-[2,3']BIINDOLYLIDENE-3,2'-DIONE-3-OXIME C₁₆ H₁₁ N₃ O₂ HBDSHCUSXQATPO-BGBJRWHRSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.300 (Depositor), 0.317 (DCC)
R-Value Work: 0.247 (Depositor), 0.276 (DCC)
R-Value Observed: 0.249 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.133	α = 90
b = 64.133	β = 90
c = 201.153	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-09-04

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-09-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-18
Changes: Refinement description
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description