5XRB

Crystal Structure of the human Hsp90-alpha N-domain bound to the hsp90 inhibitor FJ5

PDB DOI: https://doi.org/10.2210/pdb5XRB/pdb

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

Deposited: 2017-06-08 Released: 2018-07-04
Deposition Author(s): Li, J., Shi, F., Xiong, B., He, J.H.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.198
R-Value Work: 0.187
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of the human Hsp90-alpha N-domain bound to the hsp90 inhibitor FJ5

Li, J., Shi, F., Xiong, B., He, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 26.06 kDa
Atom Count: 1,773
Modelled Residue Count: 207
Deposited Residue Count: 228
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HSP 90-alpha	A	228	Homo sapiens	Mutation(s): 0 Gene Names: HSP90AA1, HSP90A, HSPC1, HSPCA EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for P07900 (Homo sapiens) Explore P07900 Go to UniProtKB: P07900
PHAROS: P07900 GTEx: ENSG00000080824
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07900
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8DU Query on 8DU 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]	N-[3-[5-chloranyl-2,4-bis(oxidanyl)phenyl]-4-(4-methoxyphenyl)-1,2-oxazol-5-yl]cyclopropanecarboxamide C₂₀ H₁₇ Cl N₂ O₅ DWCUAHBOVUBFHQ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
8DU	BindingDB: 5XRB	IC50: 53 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.198
R-Value Work: 0.187
R-Value Observed: 0.188
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.446	α = 90
b = 90.701	β = 90
c = 98.277	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHENIX	model building
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-07-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81402850

Revision History (Full details and data files)

Version 1.0: 2018-07-04
Type: Initial release
Version 1.1: 2018-11-21
Changes: Data collection, Experimental preparation
Version 1.2: 2024-03-27
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.