7F4X | pdb_00007f4x

Joint neutron and X-ray crystal structure of the nucleotide-binding domain of Hsp72 in complex with ADP

• PDB DOI: https://doi.org/10.2210/pdb7F4X/pdb

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


• Deposited: 2021-06-21 Released: 2022-06-29 
• Deposition Author(s): Yokoyama, T., Ostermann, A., Schrader, T.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.190 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

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• Method: NEUTRON DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.222 (Depositor) 
• R-Value Work: 
  0.184 (Depositor) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Neutron crystallographic analysis of the nucleotide-binding domain of Hsp72 in complex with ADP.

Yokoyama, T., Fujii, S., Ostermann, A., Schrader, T.E., Nabeshima, Y., Mizuguchi, M.

(2022) IUCrJ 9: 562-572

• DOI: https://doi.org/10.1107/S2052252522006297

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 43.24 kDa 
• Atom Count: 3,054 
• Modeled Residue Count: 378 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock 70 kDa protein 1B	A	386	Homo sapiens	Mutation(s): 0  Gene Names: HSPA1B, HSP72
UniProt & NIH Common Fund Data Resources
Find proteins for P0DMV9 (Homo sapiens) Explore P0DMV9  Go to UniProtKB:  P0DMV9
PHAROS:  P0DMV9 GTEx:  ENSG00000204388

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ADP	BindingDB:  7F4X	IC50: 280 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.190 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

• Method: NEUTRON DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.222 (Depositor) 
• R-Value Work:  0.184 (Depositor) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.677	α = 90
b = 64.618	β = 90
c = 145.593	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-06-29 
Deposition Author(s): Yokoyama, T., Ostermann, A., Schrader, T.E.

Revision History  

• Version 1.0: 2022-06-29
  Type: Initial release
  
• Version 1.1: 2022-09-14
  Changes: Database references
• Version 1.2: 2024-04-03
  Changes: Data collection, Refinement description