1Z6Y | pdb_00001z6y

Structure Of Human ADP-Ribosylation Factor-Like 5

PDB DOI: https://doi.org/10.2210/pdb1Z6Y/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2005-03-23 Released: 2005-04-05
Deposition Author(s): Choe, J., Atanassova, A., Arrowsmith, C., Edwards, A., Sundstrom, M., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.283 (Depositor), 0.280 (DCC)
R-Value Work:
0.233 (Depositor), 0.232 (DCC)
R-Value Observed:
0.235 (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 5

Atanassova, A., Choe, J., Arrowsmith, C., Edwards, A., Sundstrom, M., Bochkarev, A., Park, H.

To be published.

Macromolecule Content

Total Structure Weight: 42.39 kDa
Atom Count: 2,931
Modeled Residue Count: 338
Deposited Residue Count: 358
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosylation factor-like protein 5	A, B	179	Homo sapiens	Mutation(s): 0 Gene Names: ARL5, ARFLP5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y689 (Homo sapiens) Explore Q9Y689 Go to UniProtKB: Q9Y689
PHAROS: Q9Y689 GTEx: ENSG00000162980
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y689
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 C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.283 (Depositor), 0.280 (DCC)
R-Value Work: 0.233 (Depositor), 0.232 (DCC)
R-Value Observed: 0.235 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.657	α = 112.96
b = 48.775	β = 97.69
c = 55.905	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-04-05

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2005-04-05
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: 2023-08-23
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.