5BPL | pdb_00005bpl

Crystal structure of ADP and Pi bound human Hsp70 NBD mutant R272K.

PDB DOI: https://doi.org/10.2210/pdb5BPL/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-05-28 Released: 2016-09-14
Deposition Author(s): Narayanan, D., Engh, R.A.
Funding Organization(s): FRINAT

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.239 (Depositor), 0.241 (DCC)
R-Value Work:
0.183 (Depositor), 0.186 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Nucleotide binding to variants of the HSP70-NBD.

Narayanan, D., Pflug, A., Christopeit, T., Kyomuhendo, P., Engh, R.A.

To be published.

Macromolecule Content

Total Structure Weight: 43.79 kDa
Atom Count: 3,342
Modeled Residue Count: 380
Deposited Residue Count: 388
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock 70 kDa protein 1A	A	388	Homo sapiens	Mutation(s): 1 Gene Names: HSPA1A, HSPA1, HSX70
UniProt & NIH Common Fund Data Resources
Find proteins for P0DMV8 (Homo sapiens) Explore P0DMV8 Go to UniProtKB: P0DMV8
PHAROS: P0DMV8 GTEx: ENSG00000204389
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DMV8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF 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] Interactions & Density Focus chain B [auth A]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
ADP	BindingDB: 5BPL	IC50: 280 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.239 (Depositor), 0.241 (DCC)
R-Value Work: 0.183 (Depositor), 0.186 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.037	α = 90
b = 63.327	β = 90
c = 143.798	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
MOLREP	phasing
Aimless	data scaling
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-09-14

Deposition Author(s):

Narayanan, D.

Engh, R.A.

Funding Organization	Location	Grant Number
FRINAT	Norway	191303

Revision History (Full details and data files)

Version 1.0: 2016-09-14
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description

5BPL | pdb_00005bpl

Crystal structure of ADP and Pi bound human Hsp70 NBD mutant R272K.

Literature

Nucleotide binding to variants of the HSP70-NBD.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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