1X3S | pdb_00001x3s

Crystal structure of human Rab18 in complex with Gppnhp

• PDB DOI: https://doi.org/10.2210/pdb1X3S/pdb

• Classification: ENDOCYTOSIS/EXOCYTOSIS
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 2005-05-10 Released: 2005-11-10 
• Deposition Author(s): Kukimoto-Niino, M., Murayama, K., Chen, L., Liu, Z.J., Wang, B.C., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 
  0.210 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Crystal structure of human Rab18 in complex with Gppnhp

Kukimoto-Niino, M., Murayama, K., Chen, L., Liu, Z.J., Wang, B.C., Shirouzu, M., Yokoyama, S.

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: 22.31 kDa 
• Atom Count: 1,668 
• Modeled Residue Count: 177 
• Deposited Residue Count: 195 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-18	A	195	Homo sapiens	Mutation(s): 3  EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NP72 (Homo sapiens) Explore Q9NP72  Go to UniProtKB:  Q9NP72
PHAROS:  Q9NP72 GTEx:  ENSG00000099246

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free:  0.210 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.889	α = 90
b = 65.182	β = 91.42
c = 40.71	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-10 
Deposition Author(s): Kukimoto-Niino, M., Murayama, K., Chen, L., Liu, Z.J., Wang, B.C., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-11-10
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary