8YNR

Crystal Structure of Human Rab23 in complex with GMPPNP (1.8 Angstroms Resolution)

PDB DOI: https://doi.org/10.2210/pdb8YNR/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-03-11 Released: 2024-12-04
Deposition Author(s): Chau, Y.Y., Aik, W.S.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.231
R-Value Work: 0.203
R-Value Observed: 0.205

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

Structural basis for Rab23 activation and a loss-of-function mutation in Carpenter Syndrome

Chau, Y.Y., Liang, H., Tung, W.L., Hor, C.H.H., Aik, W.S.

To be published.

Macromolecule Content

Total Structure Weight: 19.64 kDa
Atom Count: 1,369
Modelled Residue Count: 160
Deposited Residue Count: 167
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-23	A	167	Homo sapiens	Mutation(s): 0 Gene Names: RAB23, HSPC137
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULC3 (Homo sapiens) Explore Q9ULC3 Go to UniProtKB: Q9ULC3
PHAROS: Q9ULC3 GTEx: ENSG00000112210
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9ULC3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNP (Subject of Investigation/LOI) Query on GNP 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]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.231
R-Value Work: 0.203
R-Value Observed: 0.205
Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.677	α = 90
b = 61.333	β = 90
c = 70.601	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data scaling
CrysalisPro	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-12-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	Hong Kong	HKBU Faculty of Science Seed Money

Revision History (Full details and data files)

Version 1.0: 2024-12-04
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.