4NC6 | pdb_00004nc6

Tbc domain of human rab gtpase-activating protein 1

• PDB DOI: https://doi.org/10.2210/pdb4NC6/pdb

• Classification: HYDROLASE ACTIVATOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-10-24 Released: 2015-08-19 
• Deposition Author(s): Janowski, R., Boutin, M., Coll, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.215 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Tbc domain of human rab gtpase-activating protein 1

Janowski, R., Boutin, M., Coll, M.

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: 37.2 kDa 
• Atom Count: 2,841 
• Modeled Residue Count: 291 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rab GTPase-activating protein 1	A	314	Homo sapiens	Mutation(s): 0  Gene Names: RABGAP1, HSPC094
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3P9 (Homo sapiens) Explore Q9Y3P9  Go to UniProtKB:  Q9Y3P9
PHAROS:  Q9Y3P9 GTEx:  ENSG00000011454

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.215 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.15	α = 90
b = 51.39	β = 90
c = 132.22	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-19 
Deposition Author(s): Janowski, R., Boutin, M., Coll, M.

Revision History  

• Version 1.0: 2015-08-19
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description