3M3Z | pdb_00003m3z

Crystal structure of HSC70/BAG1 in complex with small molecule inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3M3Z/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-03-10 Released: 2011-01-26 
• Deposition Author(s): Dokurno, P., Surgenor, A.E., Shaw, T., Macias, A.T., Massey, A.J., Williamson, D.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.293 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

Adenosine-Derived Inhibitors of 78 kDa Glucose Regulated Protein (Grp78) ATPase: Insights into Isoform Selectivity.

Macias, A.T., Williamson, D.S., Allen, N., Borgognoni, J., Clay, A., Daniels, Z., Dokurno, P., Drysdale, M.J., Francis, G.L., Graham, C.J., Howes, R., Matassova, N., Murray, J.B., Parsons, R., Shaw, T., Surgenor, A.E., Terry, L., Wang, Y., Wood, M., Massey, A.J.

(2011) J Med Chem 54: 4034-4041

• PubMed: 21526763 
• DOI: https://doi.org/10.1021/jm101625x
• Primary Citation of Related Structures:  
  3LDL, 3LDN, 3LDO, 3LDP, 3LDQ, 3M3Z


• PubMed Abstract: 
  

  78 kDa glucose-regulated protein (Grp78) is a heat shock protein (HSP) involved in protein folding that plays a role in cancer cell proliferation. Binding of adenosine-derived inhibitors to Grp78 was characterized by surface plasmon resonance and isothermal titration calorimetry. The most potent compounds were 13 (VER-155008) with K(D) = 80 nM and 14 with K(D) = 60 nM. X-ray crystal structures of Grp78 bound to ATP, ADPnP, and adenosine derivative 10 revealed differences in the binding site between Grp78 and homologous proteins.

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Organizational Affiliation: 

Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, CB21 6GB, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.6 kDa 
• Atom Count: 4,185 
• Modeled Residue Count: 488 
• Deposited Residue Count: 495 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock cognate 71 kDa protein	A	381	Homo sapiens	Mutation(s): 0  Gene Names: HSPA8, HSC70, HSP73, HSPA10 EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for P11142 (Homo sapiens) Explore P11142  Go to UniProtKB:  P11142
PHAROS:  P11142 GTEx:  ENSG00000109971

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BAG family molecular chaperone regulator 1	B	114	Homo sapiens	Mutation(s): 0  Gene Names: BAG1, HAP
UniProt & NIH Common Fund Data Resources
Find proteins for Q99933 (Homo sapiens) Explore Q99933  Go to UniProtKB:  Q99933
PHAROS:  Q99933 GTEx:  ENSG00000107262

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3F5	C [auth A]	5'-O-(2-amino-2-oxoethyl)-8-(methylamino)adenosine C13 H19 N7 O5 YTEPWBADDXGTBX-JJNLEZRASA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3F5	BindingDB:  3M3Z	Ki: 1850 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.293 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.776	α = 90
b = 120.969	β = 106.78
c = 53.537	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-26 
Deposition Author(s): Dokurno, P., Surgenor, A.E., Shaw, T., Macias, A.T., Massey, A.J., Williamson, D.S.

Revision History  

• Version 1.0: 2011-01-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary