3Q5K | pdb_00003q5k

Crystal structure of the amino-terminal domain of HSP90 from Leishmania major, LMJF33.0312:M1-K213 in the presence of an inhibitor

PDB DOI: https://doi.org/10.2210/pdb3Q5K/pdb

Classification: CHAPERONE
Organism(s): Leishmania major
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-12-28 Released: 2011-02-23
Deposition Author(s): Wernimont, A.K., Tempel, W., Lin, Y.H., Hutchinson, A., MacKenzie, F., Fairlamb, A., Cossar, D., Zhao, Y., Schapira, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Ferguson, M.A.J., Hui, R., Pizarro, J.C., Hills, T., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.261 (Depositor), 0.277 (DCC)
R-Value Work:
0.242 (Depositor), 0.257 (DCC)
R-Value Observed:
0.243 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the amino-terminal domain of HSP90 from Leishmania major, LMJF33.0312:M1-K213 in the presence of an inhibitor

Wernimont, A.K., Tempel, W., Lin, Y.H., Hutchinson, A., MacKenzie, F., Fairlamb, A., Cossar, D., Zhao, Y., Schapira, M., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Weigelt, J., Ferguson, M.A.J., Hui, R., Pizarro, J.C., Hills, T.

To be published.

Macromolecule Content

Total Structure Weight: 26.55 kDa
Atom Count: 1,578
Modeled Residue Count: 213
Deposited Residue Count: 231
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein 83-1	A	231	Leishmania major	Mutation(s): 0 Gene Names: LMJF33.0312
UniProt
Find proteins for Q4Q4I6 (Leishmania major) Explore Q4Q4I6 Go to UniProtKB: Q4Q4I6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4Q4I6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D1U Query on D1U 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]	4-[6,6-dimethyl-4-oxo-3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]-2-{[2-(methylsulfanyl)ethyl]amino}benzamide C₂₀ H₂₃ F₃ N₄ O₂ S ISQWIAFSRBRSHC-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.261 (Depositor), 0.277 (DCC)
R-Value Work: 0.242 (Depositor), 0.257 (DCC)
R-Value Observed: 0.243 (Depositor)

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.258	α = 90
b = 73.258	β = 90
c = 213.604	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
TNT	refinement
PDB_EXTRACT	data extraction
BUSTER	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-02-23

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2011-02-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations