6S5F | pdb_00006s5f

Structure of the human RAB39B in complex with GMPPNP

• PDB DOI: https://doi.org/10.2210/pdb6S5F/pdb

• Classification: STRUCTURAL GENOMICS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-01 Released: 2020-07-22 
• Deposition Author(s): Diaz-Saez, L., Jung, S., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Huber, K., Structural Genomics Consortium (SGC)
• Funding Organization(s): Innovative Medicines Initiative

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Structure of the human RAB39B in complex with GMPPNP

Diaz-Saez, L., Jung, S., Huber, K., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.66 kDa 
• Atom Count: 1,767 
• Modeled Residue Count: 188 
• Deposited Residue Count: 208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-39B	A	208	Homo sapiens	Mutation(s): 0  Gene Names: RAB39B EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q96DA2 (Homo sapiens) Explore Q96DA2  Go to UniProtKB:  Q96DA2
PHAROS:  Q96DA2 GTEx:  ENSG00000155961

Small Molecules

Ligands 4 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
GLY	B [auth A]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.725	α = 90
b = 35.285	β = 107.51
c = 53.605	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
DIALS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-22 
Deposition Author(s): Diaz-Saez, L., Jung, S., von Delft, F., Arrowsmith, C.H., Edwards, A., Bountra, C., Huber, K., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Innovative Medicines Initiative	United Kingdom	--

Revision History  

• Version 1.0: 2020-07-22
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Advisory, Data collection, Database references, Refinement description