3DWD | pdb_00003dwd

Crystal structure of the ArfGAP domain of human ARFGAP1

• PDB DOI: https://doi.org/10.2210/pdb3DWD/pdb

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


• Deposited: 2008-07-22 Released: 2008-08-05 
• Deposition Author(s): Nedyalkova, L., Tong, Y., Tempel, W., Landry, R., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Wilkstrom, M., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.273 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.234 (Depositor) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the ArfGAP domain of human ARFGAP1

Nedyalkova, L., Tong, Y., Tempel, W., Landry, R., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Wilkstrom, M., Bochkarev, A., Park, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.83 kDa 
• Atom Count: 1,772 
• Modeled Residue Count: 230 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor GTPase-activating protein 1	A, B	147	Homo sapiens	Mutation(s): 0  Gene Names: ARFGAP1, ARF1GAP
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N6T3 (Homo sapiens) Explore Q8N6T3  Go to UniProtKB:  Q8N6T3
PHAROS:  Q8N6T3 GTEx:  ENSG00000101199

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNX	D [auth A], F [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.273 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.234 (Depositor) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.422	α = 90
b = 82.422	β = 90
c = 81.008	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DM	phasing
MolProbity	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-05 
Deposition Author(s): Nedyalkova, L., Tong, Y., Tempel, W., Landry, R., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Wilkstrom, M., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-08-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary