6G8Y | pdb_00006g8y

Crystal Structures of the Single PDZ Domains from GRASP65 and their Interaction with the Golgin GM130

PDB DOI: https://doi.org/10.2210/pdb6G8Y/pdb

Classification: PROTEIN BINDING
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-04-10 Released: 2019-04-24
Deposition Author(s): Jurk, C.M., Roske, Y., Heinemann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.210 (Depositor), 0.208 (DCC)
R-Value Work:
0.163 (Depositor), 0.163 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6G8Y

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structures of the Single PDZ Domains from GRASP65 and their Interaction with the Golgin GM130

Jurk, C.M., Roske, Y., Heinemann, U.

(2018) Croat Chem Acta

DOI: https://doi.org/10.5562/cca3341

Macromolecule Content

Total Structure Weight: 10.85 kDa
Atom Count: 911
Modeled Residue Count: 92
Deposited Residue Count: 92
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylated cis-Golgi protein, involved in ER-to-Golgi transport	A	92	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: GRH1, SCKG_0028
UniProt
Find proteins for Q04410 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04410 Go to UniProtKB: Q04410
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q04410
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.210 (Depositor), 0.208 (DCC)
R-Value Work: 0.163 (Depositor), 0.163 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.443	α = 90
b = 53.443	β = 90
c = 50.923	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
Auto-Rickshaw	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-04-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-04-24
Type: Initial release
Version 1.1: 2020-05-06
Changes: Database references
Version 1.2: 2024-05-08
Changes: Data collection, Database references

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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.