4ILE | pdb_00004ile

Structure of human ADP-ribosylation factor-like 8A binding to GDP

• PDB DOI: https://doi.org/10.2210/pdb4ILE/pdb

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


• Deposited: 2012-12-31 Released: 2014-01-01 
• Deposition Author(s): Xie, Y., Ren, J., Cheng, Z., Qian, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 
  0.270 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Structure of human ADP-ribosylation factor-like 8A binding to GDP

Xie, Y., Ren, J., Cheng, Z., Qian, H.

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: 21.9 kDa 
• Atom Count: 1,504 
• Modeled Residue Count: 176 
• Deposited Residue Count: 184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor-like protein 8A	A	184	Homo sapiens	Mutation(s): 0  Gene Names: ARL8A, ARL10B, GIE2
UniProt & NIH Common Fund Data Resources
Find proteins for Q96BM9 (Homo sapiens) Explore Q96BM9  Go to UniProtKB:  Q96BM9
PHAROS:  Q96BM9 GTEx:  ENSG00000143862

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-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: 2.68 Å
• R-Value Free:  0.270 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.032	α = 90
b = 37.374	β = 90
c = 39.315	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-01 
Deposition Author(s): Xie, Y., Ren, J., Cheng, Z., Qian, H.

Revision History  

• Version 1.0: 2014-01-01
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-11-20
  Changes: Structure summary