2GF9 | pdb_00002gf9

Crystal structure of human RAB3D in complex with GDP

• PDB DOI: https://doi.org/10.2210/pdb2GF9/pdb

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


• Deposited: 2006-03-21 Released: 2006-05-02 
• Deposition Author(s): Hong, B., Wang, J., Shen, L., Tempel, W., Landry, R., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.185 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.165 (DCC) 

Starting Model: experimental

Literature

Crystal structure of human RAB3D in complex with GDP

Hong, B., Wang, J., Shen, L., Tempel, W., Landry, R., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Bochkarev, A., Park, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.14 kDa 
• Atom Count: 1,653 
• Modeled Residue Count: 176 
• Deposited Residue Count: 189 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-3D	A	189	Homo sapiens	Mutation(s): 0  Gene Names: RAB3D, GOV, RAB16 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for O95716 (Homo sapiens) Explore O95716  Go to UniProtKB:  O95716
PHAROS:  O95716 GTEx:  ENSG00000105514

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	E [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNX	C [auth A], D [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.185 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.165 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.7	α = 90
b = 63.222	β = 90
c = 67.695	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-02 
Deposition Author(s): Hong, B., Wang, J., Shen, L., Tempel, W., Landry, R., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2006-05-02
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description