3BFK

Crystal structure of Plasmodium falciparum Rab11a in complex with GDP

PDB DOI: https://doi.org/10.2210/pdb3BFK/pdb

Classification: HYDROLASE
Organism(s): Plasmodium falciparum 3D7
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-11-21 Released: 2007-12-04
Deposition Author(s): Pizarro, J.C., Sukumar, D., Hassanali, A., Lin, L., Wernimont, A.K., Lew, J., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Sundstrom, M., Bochkarev, A., Hui, R., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.259
R-Value Work: 0.218
R-Value Observed: 0.220

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Plasmodium falciparum Rab11a in complex with GDP.

Pizarro, J.C., Sukumar, D., Hassanali, A., Lin, L., Wernimont, A.K., Lew, J., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Sundstrom, M., Bochkarev, A., Hui, R.

To be published.

Macromolecule Content

Total Structure Weight: 105.93 kDa
Atom Count: 7,472
Modelled Residue Count: 825
Deposited Residue Count: 905
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Small GTPase Rab11	A, B, C, D, E	181	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: PF13_0119 EC: 3.6.5.2
UniProt
Find proteins for Q76NM4 (Plasmodium falciparum (isolate 3D7)) Explore Q76NM4 Go to UniProtKB: Q76NM4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q76NM4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain M [auth E] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E]	F [auth A], G [auth B], J [auth C], L [auth D], M [auth E]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth E] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C]	H [auth B], I [auth B], K [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Interactions & Density Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.259
R-Value Work: 0.218
R-Value Observed: 0.220
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.49	α = 90
b = 48.371	β = 92.36
c = 119.236	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-12-04

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-12-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, 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

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3BFK

Crystal structure of Plasmodium falciparum Rab11a in complex with GDP

Crystal structure of Plasmodium falciparum Rab11a in complex with GDP.

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)