8XTU | pdb_00008xtu

Crystal Structure of Rab5b GTPase domain from Leishmania donovani in complex with GDP

PDB DOI: https://doi.org/10.2210/pdb8XTU/pdb

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

Deposited: 2024-01-11 Released: 2025-01-15
Deposition Author(s): Zohib, M., Pal, R.K., Biswal, B.K., Arora, A.
Funding Organization(s): Council of Scientific & Industrial Research (CSIR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.263 (Depositor), 0.263 (DCC)
R-Value Work:
0.216 (Depositor), 0.219 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of Rab5b GTPase domain from Leishmania donovani in complex with GDP

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

To be published.

Macromolecule Content

Total Structure Weight: 18.95 kDa
Atom Count: 1,195
Modeled Residue Count: 156
Deposited Residue Count: 168
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rab5	A	168	Leishmania donovani	Mutation(s): 4
UniProt
Find proteins for Q6VN21 (Leishmania donovani) Explore Q6VN21 Go to UniProtKB: Q6VN21
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6VN21
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 C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.263 (Depositor), 0.263 (DCC)
R-Value Work: 0.216 (Depositor), 0.219 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.066	α = 90
b = 61.861	β = 90
c = 73.635	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Council of Scientific & Industrial Research (CSIR)	India	CSIR NCP MLP 2031

Revision History (Full details and data files)

Version 1.0: 2025-01-15
Type: Initial release

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.