Download MendeleyCrystal structure of human GRP78 in complex with (2R,3R,4S,5R)-2-(6-amino-8-((2-chlorobenzyl)amino)-9H-purin-9-yl)-5-(hydroxymethyl)tetrahydrofuran-3,4-diol
Chen, Y., Antoshchenko, T., Smil, D., Zepeda, C., Huang, Y., Park, H.W.To be published.
6DWS | pdb_00006dws
Crystal structure of human GRP78 in complex with (2R,3R,4S,5R)-2-(6-amino-8-((2-chlorobenzyl)amino)-9H-purin-9-yl)-5-(hydroxymethyl)tetrahydrofuran-3,4-diol
- PDB DOI: https://doi.org/10.2210/pdb6DWS/pdb
- Classification: chaperone, transferase
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2018-06-27 Released: 2019-07-03
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.248 (Depositor), 0.250 (DCC)
- R-Value Work: 0.213 (Depositor), 0.220 (DCC)
- R-Value Observed: 0.215 (Depositor)
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Endoplasmic reticulum chaperone BiP | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P11021 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| HFY Query on HFY | C [auth A], E [auth B] | 8-{[(2-chlorophenyl)methyl]amino}adenosine C17 H19 Cl N6 O4 HXRSLQGBEUJHPP-XNIJJKJLSA-N |  | ||
| MG Query on MG | D [auth A], F [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.248 (Depositor), 0.250 (DCC)
- R-Value Work: 0.213 (Depositor), 0.220 (DCC)
- R-Value Observed: 0.215 (Depositor)
Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 54.916 | α = 90 |
| b = 74.611 | β = 98.1 |
| c = 86.848 | γ = 90 |
| Software Name | Purpose |
|---|---|
| BUSTER | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| XDS | data scaling |
| BUSTER | phasing |
Entry History
Deposition Data
- Released Date: 2019-07-03 Deposition Author(s): Chen, Y., Antoshchenko, T., Smil, D., Zepeda, C., Huang, Y., Park, H.W.
Revision History (Full details and data files)
- Version 1.0: 2019-07-03
Type: Initial release - Version 1.1: 2024-03-13
Changes: Data collection, Database references, Derived calculations
