6MF9 | pdb_00006mf9

Crystal structure of CGD4-650 with compound BI2536

PDB DOI: https://doi.org/10.2210/pdb6MF9/pdb

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

Deposited: 2018-09-10 Released: 2018-10-10
Deposition Author(s): Dong, A., Lin, Y.L., Hou, D., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Vedadi, M., Hui, R., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free:
0.226 (Depositor), 0.225 (DCC)
R-Value Work:
0.182 (Depositor), 0.190 (DCC)
R-Value Observed:
0.183 (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 CGD4-650 with compound BI2536

Dong, A., Lin, Y.L., Hou, D., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Vedadi, M., Hui, R., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 38.94 kDa
Atom Count: 2,268
Modeled Residue Count: 253
Deposited Residue Count: 334
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ZnKn (C2HC)+Athook+bromo domain protein, Taf250, transcription initiation factor IID	A, B	167	Cryptosporidium parvum Iowa II	Mutation(s): 0 Gene Names: cgd4_650
UniProt
Find proteins for Q5CQH9 (Cryptosporidium parvum (strain Iowa II)) Explore Q5CQH9 Go to UniProtKB: Q5CQH9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5CQH9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
R78 Query on R78 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide C₂₈ H₃₉ N₇ O₃ XQVVPGYIWAGRNI-JOCHJYFZSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.226 (Depositor), 0.225 (DCC)
R-Value Work: 0.182 (Depositor), 0.190 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.785	α = 90
b = 89.869	β = 90
c = 95.635	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BALBES	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-10-10

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2018-10-10
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description, Structure summary

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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.