3PRY | pdb_00003pry

Crystal structure of the middle domain of human HSP90-beta refined at 2.3 A resolution

PDB DOI: https://doi.org/10.2210/pdb3PRY/pdb

Classification: CHAPERONE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-11-30 Released: 2010-12-15
Deposition Author(s): Chaikuad, A., Pilka, E., Sharpe, T.D., Cooper, C.D.O., Phillips, C., Berridge, G., Ayinampudi, V., Fedorov, O., Keates, T., Thangaratnarajah, C., Zimmermann, T., Vollmar, M., Yue, W.W., Che, K.H., Krojer, T., Muniz, J.R.C., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Bullock, A., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free:
0.217 (Depositor), 0.234 (DCC)
R-Value Work:
0.172 (Depositor), 0.191 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the middle domain of human HSP90-beta refined at 2.3 A resolution

Chaikuad, A., Pilka, E., Sharpe, T.D., Cooper, C.D.O., Phillips, C., Berridge, G., Ayinampudi, V., Fedorov, O., Keates, T., Thangaratnarajah, C., Zimmermann, T., Vollmar, M., Yue, W.W., Che, K.H., Krojer, T., Muniz, J.R.C., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A., Bullock, A., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 96.09 kDa
Atom Count: 6,396
Modeled Residue Count: 756
Deposited Residue Count: 804
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HSP 90-beta	A, B, C	268	Homo sapiens	Mutation(s): 0 Gene Names: HSP90AB1, HSP90B, HSPC2, HSPCB
UniProt & NIH Common Fund Data Resources
Find proteins for P08238 (Homo sapiens) Explore P08238 Go to UniProtKB: P08238
PHAROS: P08238 GTEx: ENSG00000096384
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08238
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B]	D [auth A], E [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain I [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B]	G [auth B], H [auth B], I [auth B], J [auth B], K [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.217 (Depositor), 0.234 (DCC)
R-Value Work: 0.172 (Depositor), 0.191 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.71	α = 90
b = 73.71	β = 90
c = 149.05	γ = 120

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-12-15

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2010-12-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description