7F4X

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.190
R-Value Work: 0.166
R-Value Observed: 0.167

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

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DMV9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain B [auth A]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A]
NA (Subject of Investigation/LOI) Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.190
R-Value Work: 0.166
R-Value Observed: 0.167
Space Group: P 2₁ 2₁ 2₁

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2022-06-29

Deposition Author(s):

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.