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.

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), 0.178 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

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

Xie, Y., Ren, J., Cheng, Z., Qian, H.

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96BM9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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), 0.178 (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

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Entry History

Deposition Data

Released Date: 2014-01-01

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.