9JB3 | pdb_00009jb3

Crystal structure of DH domain of human FGD6

• PDB DOI: https://doi.org/10.2210/pdb9JB3/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-26 Released: 2025-09-03 
• Deposition Author(s): Liu, Z.C., Chuan, J.L., Wang, G.G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the DH domain of human FGD6

Liu, Z.C., Chuan, J.L., Wang, G.G.

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: 22.11 kDa 
• Atom Count: 1,792 
• Modeled Residue Count: 189 
• Deposited Residue Count: 189 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FYVE, RhoGEF and PH domain-containing protein 6	A	189	Homo sapiens	Mutation(s): 0  Gene Names: FGD6, KIAA1362, ZFYVE24
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZV73 (Homo sapiens) Explore Q6ZV73  Go to UniProtKB:  Q6ZV73
PHAROS:  Q6ZV73 GTEx:  ENSG00000180263

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.197	α = 90
b = 74.197	β = 90
c = 40.398	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Liu, Z.C., Chuan, J.L., Wang, G.G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release