8JQU

Crystal structure of GppNHp bound GTPase domain of Rab5a from Leishmania donovani

• PDB DOI: https://doi.org/10.2210/pdb8JQU/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Leishmania donovani
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2023-06-14 Released: 2024-06-19 
• Deposition Author(s): Pandey, D., Zohib, M., Pal, R.K., Biswal, B.K., Arora, A.
• Funding Organization(s): Council of Scientific & Industrial Research (CSIR), Global Challenges Research Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.203 
• R-Value Work: 0.162 

Literature

Crystal structure of GppNHp bound GTPase domain of Rab5a from Leishmania donovani

Pandey, D., Zohib, M., Pal, R.K., Biswal, B.K., Arora, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 19.85 kDa 
• Atom Count: 1,482 
• Modelled Residue Count: 164 
• Deposited Residue Count: 175 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rab5a	A	175	Leishmania donovani	Mutation(s): 4  Gene Names: Rab5a
UniProt
Find proteins for A0A109NYM0 (Leishmania donovani) Explore A0A109NYM0  Go to UniProtKB:  A0A109NYM0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP (Subject of Investigation/LOI)	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.203 
• R-Value Work: 0.162 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.552	α = 90
b = 42.266	β = 103.387
c = 37.777	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-19 
Deposition Author(s): Pandey, D., Zohib, M., Pal, R.K., Biswal, B.K., Arora, A.

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Funding Organization	Location	Grant Number
Council of Scientific & Industrial Research (CSIR)	India	CSIR NCP MLP2031
Global Challenges Research Fund	United Kingdom	MR/P027989/1

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release