3EB0

Crystal Structure of cgd4_240 from cryptosporidium Parvum in complex with indirubin E804

PDB DOI: https://doi.org/10.2210/pdb3EB0/pdb

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

Deposited: 2008-08-26 Released: 2008-09-16
Deposition Author(s): Wernimont, A.K., Fedorov, O., Lam, A., Ali, A., Zhao, Y., Lew, J., Wasney, G., Vedadi, M., Kozieradzki, I., Schapira, M., Bochkarev, A., Wilstrom, M., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Hui, R., Lin, Y.H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.295
R-Value Work: 0.238
R-Value Observed: 0.240

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of cgd4_240 from cryptosporidium Parvum in complex with indirubin E804

Wernimont, A.K., Fedorov, O., Lam, A., Ali, A., Zhao, Y., Lew, J., Wasney, G., Vedadi, M., Kozieradzki, I., Schapira, M., Bochkarev, A., Wilstrom, M., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Hui, R., Lin, Y.H.

To be published.

Macromolecule Content

Total Structure Weight: 88.76 kDa
Atom Count: 5,221
Modelled Residue Count: 623
Deposited Residue Count: 766
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B [auth C]	383	Cryptosporidium parvum Iowa II	Mutation(s): 0 Gene Names: cgd4_240
UniProt
Find proteins for A3FQN0 (Cryptosporidium parvum (strain Iowa II)) Explore A3FQN0 Go to UniProtKB: A3FQN0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A3FQN0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DRK Query on DRK Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth C] MOL2 format, chain C [auth A] MOL2 format, chain F [auth C]	C [auth A], F [auth C]	3-({[(3S)-3,4-dihydroxybutyl]oxy}amino)-1H,2'H-2,3'-biindol-2'-one C₂₀ H₁₉ N₃ O₄ CKLAPOFDFZKCPB-LBPRGKRZSA-N		Interactions Focus chain C [auth A] Focus chain F [auth C] Interactions & Density Focus chain C [auth A] Focus chain F [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth C] SDF format, chain H [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth C] MOL2 format, chain H [auth C]	D [auth A], E [auth A], G [auth C], H [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth C] Focus chain H [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth C] Focus chain H [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on PTR	A, B [auth C]	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.295
R-Value Work: 0.238
R-Value Observed: 0.240
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.101	α = 90
b = 138.366	β = 90
c = 43.261	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-09-16

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2008-09-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-11-15
Changes: Data collection

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3EB0

Crystal Structure of cgd4_240 from cryptosporidium Parvum in complex with indirubin E804

Crystal Structure of cgd4_240 from cryptosporidium Parvum in complex with indirubin E804

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)