6DFO | pdb_00006dfo

Crystal structure of human GRP78 in complex with 8-bromoadenosine

PDB DOI: https://doi.org/10.2210/pdb6DFO/pdb

Classification: CHAPERONE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-05-15 Released: 2019-05-15
Deposition Author(s): Ferrie, R.P., Chen, Y., Antoshchenko, T., Cooney, O.M., Huang, Y., Park, H.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free:
0.251 (Depositor), 0.247 (DCC)
R-Value Work:
0.187 (Depositor), 0.189 (DCC)
R-Value Observed:
0.190 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of human GRP78 in complex with 8-bromoadenosine

Ferrie, R.P., Chen, Y., Antoshchenko, T., Cooney, O.M., Huang, Y., Park, H.W.

To be published.

Macromolecule Content

Total Structure Weight: 85 kDa
Atom Count: 6,152
Modeled Residue Count: 762
Deposited Residue Count: 764
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoplasmic reticulum chaperone BiP	A, B	382	Homo sapiens	Mutation(s): 0 Gene Names: HSPA5, GRP78 EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for P11021 (Homo sapiens) Explore P11021 Go to UniProtKB: P11021
PHAROS: P11021 GTEx: ENSG00000044574
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11021
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GBA Query on GBA 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]	8-bromoadenosine C₁₀ H₁₂ Br N₅ O₄ VJUPMOPLUQHMLE-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: 2.54 Å
R-Value Free: 0.251 (Depositor), 0.247 (DCC)
R-Value Work: 0.187 (Depositor), 0.189 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.556	α = 90
b = 74.734	β = 98.78
c = 89.67	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-05-15

Deposition Author(s):

Antoshchenko, T.

Revision History (Full details and data files)

Version 1.0: 2019-05-15
Type: Initial release
Version 1.1: 2024-03-13
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.