4YY8

Crystal Structure Analysis of Kelch protein from Plasmodium falciparum

PDB DOI: https://doi.org/10.2210/pdb4YY8/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Plasmodium falciparum
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2015-03-23 Released: 2015-04-01
Deposition Author(s): Jiang, D.Q., Tempel, W., Loppnau, P., Graslund, S., He, H., Ravichandran, M., Seitova, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., El Bakkouri, M., Senisterra, G., Osman, K.T., Lovato, D.V., Hui, R., Hutchinson, A., Lin, Y.H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.207
R-Value Work: 0.175
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure Analysis of Kelch protein from Plasmodium falciparum.

Jiang, D.Q., Tempel, W., Loppnau, P., Graslund, S., He, H., Ravichandran, M., Seitova, A., Arrowsmith, C.H., Edwards, A.M., Bountra, C., El Bakkouri, M., Senisterra, G., Osman, K.T., Lovato, D.V., Hui, R., Hutchinson, A., Lin, Y.H.

To be published.

Macromolecule Content

Total Structure Weight: 89.02 kDa
Atom Count: 6,510
Modelled Residue Count: 750
Deposited Residue Count: 778
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch protein	A, B	389	Plasmodium falciparum	Mutation(s): 0 Gene Names: PF13_0238
UniProt
Find proteins for A0A077LQB4 (Plasmodium falciparum) Explore A0A077LQB4 Go to UniProtKB: A0A077LQB4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A077LQB4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain IA [auth B] SDF format, chain LA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain LA [auth B]	IA [auth B] JA [auth B] KA [auth B] LA [auth B] U [auth A] IA [auth B], JA [auth B], KA [auth B], LA [auth B], U [auth A], V [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain U [auth A] Focus chain V [auth A]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain I [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain CA [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth A] SDF format, chain T [auth A] SDF format, chain W [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth A] MOL2 format, chain T [auth A] MOL2 format, chain W [auth B]	AA [auth B] BA [auth B] C [auth A] CA [auth B] D [auth A] AA [auth B], BA [auth B], C [auth A], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth A] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth A] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.207
R-Value Work: 0.175
R-Value Observed: 0.177
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.189	α = 90
b = 117.02	β = 113.88
c = 74.566	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-04-01

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2015-04-01
Type: Initial release
Version 1.1: 2015-04-22
Changes: Database references, Structure summary
Version 1.2: 2015-07-22
Changes: Database references, Structure summary
Version 1.3: 2017-11-01
Changes: Author supporting evidence, Derived calculations, Source and taxonomy
Version 1.4: 2023-09-27
Changes: Data collection, Database references, Refinement description