6PBG | pdb_00006pbg

Crystal structure of WD-repeat domain of human coatomer subunit Alpha (COPA)

PDB DOI: https://doi.org/10.2210/pdb6PBG/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2019-06-13 Released: 2019-06-26
Deposition Author(s): Halabelian, L., Zeng, H., Dong, A., Loppnau, P., Seitova, A., Hutchinson, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.218 (Depositor), 0.228 (DCC)
R-Value Work:
0.171 (Depositor), 0.181 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of W repeat domain of human coatomer subunit Alpha (COPA)

Halabelian, L., Zeng, H., Dong, A., Loppnau, P., Seitova, A., Hutchinson, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 37.22 kDa
Atom Count: 2,722
Modeled Residue Count: 303
Deposited Residue Count: 321
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coatomer subunit alpha	A	321	Homo sapiens	Mutation(s): 0 Gene Names: COPA
UniProt & NIH Common Fund Data Resources
Find proteins for P53621 (Homo sapiens) Explore P53621 Go to UniProtKB: P53621
PHAROS: P53621 GTEx: ENSG00000122218
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53621
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TLA Query on TLA 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]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	UNKNOWN ATOM OR ION X		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.218 (Depositor), 0.228 (DCC)
R-Value Work: 0.171 (Depositor), 0.181 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.633	α = 90
b = 85.452	β = 107.04
c = 47.913	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data processing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-06-26

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2019-06-26
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, 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.