7F4Z

X-ray crystal structure of Y149A mutated Hsp72-NBD in complex with ADP

• PDB DOI: https://doi.org/10.2210/pdb7F4Z/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-06-21 Released: 2022-06-29 
• Deposition Author(s): Yokoyama, T., Fujii, S., Nabeshima, Y., Mizuguchi, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.216 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

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: 43.29 kDa 
• Atom Count: 3,313 
• Modelled 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): 1  Gene Names: HSPA1B, HSP72
UniProt & NIH Common Fund Data Resources
Find proteins for P0DMV9 (Homo sapiens) Explore P0DMV9  Go to UniProtKB:  P0DMV9
GTEx:  ENSG00000204388

Small Molecules

Ligands 5 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
PO4 (Subject of Investigation/LOI)	F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
K (Subject of Investigation/LOI)	E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.216 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.85	α = 90
b = 63.599	β = 90
c = 144.142	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-06-29 
Deposition Author(s): Yokoyama, T., Fujii, S., Nabeshima, Y., Mizuguchi, M.

Revision History  

• Version 1.0: 2022-06-29
  Type: Initial release
  
• Version 1.1: 2022-09-14
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description