3HZJ | pdb_00003hzj

Crystal structure of the RabGAP domain of the RABGAP1L protein

• PDB DOI: https://doi.org/10.2210/pdb3HZJ/pdb

• Classification: Hydrolase Activator
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-23 Released: 2009-07-14 
• Deposition Author(s): Nedyalkova, L., Tempel, W., Tong, Y., Zhong, N., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.274 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.244 (Depositor) 
• R-Value Observed: 
  0.245 (Depositor) 

Literature

Crystal structure of the RabGAP domain of the RABGAP1L protein

Nedyalkova, L., Tempel, W., Tong, Y., Zhong, N., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 110.15 kDa 
• Atom Count: 6,473 
• Modeled Residue Count: 831 
• Deposited Residue Count: 930 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAB GTPase-activating protein 1-like	A, B, C	310	Homo sapiens	Mutation(s): 0  Gene Names: RABGAP1L, HHL, KIAA0471
UniProt & NIH Common Fund Data Resources
Find proteins for Q5R372 (Homo sapiens) Explore Q5R372  Go to UniProtKB:  Q5R372
PHAROS:  Q5R372 GTEx:  ENSG00000152061

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	AA [auth C], BA [auth C], CA [auth C], D [auth A], DA [auth C], E [auth A], EA [auth C], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	UNKNOWN ATOM OR ION X

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.274 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.244 (Depositor) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.086	α = 90
b = 64.571	β = 90
c = 290.255	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-14 
Deposition Author(s): Nedyalkova, L., Tempel, W., Tong, Y., Zhong, N., MacKenzie, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary