3H80 | pdb_00003h80

Crystal structure of the amino-terminal domain of HSP90 from Leishmania major, LmjF33.0312:M1-K213

PDB DOI: https://doi.org/10.2210/pdb3H80/pdb

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

Deposited: 2009-04-28 Released: 2009-05-26
Deposition Author(s): Wernimont, A.K., Tempel, W., Lin, Y.H., Hutchinson, A., Mackenzie, F., Fairlamb, A., Kozieradzki, I., Cossar, D., Zhao, Y., Schapira, M., Bochkarev, A., Arrowsmith, C.H., Bountra, C., Weigelt, J., Edwards, A.M., Ferguson, M.A.J., Hui, R., Pizarro, J.C., Hills, T., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.273 (Depositor), 0.268 (DCC)
R-Value Work:
0.194 (Depositor), 0.191 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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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 amino-terminal domain of HSP90 from Leishmania major, LmjF33.0312:M1-K213

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

To be published.

Macromolecule Content

Total Structure Weight: 27.1 kDa
Atom Count: 1,934
Modeled Residue Count: 214
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 strain Friedlin	Mutation(s): 0 Gene Names: LmjF33.0312, LmjF33.0314, LmjF33.0316, LmjF33.0320, LmjF33.0323, LmjF33.0326, LmjF33.0333, LmjF33.0336, LmjF33.0340, LmjF33.0343... LmjF33.0312, LmjF33.0314, LmjF33.0316, LmjF33.0320, LmjF33.0323, LmjF33.0326, LmjF33.0333, LmjF33.0336, LmjF33.0340, LmjF33.0343, LmjF33.0346, LmjF33.0350, LmjF33.0355, LmjF33.0360, LmjF33.0365
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain J [auth A] MOL2 format, chain B [auth A] MOL2 format, chain J [auth A] mmCIF format, chain B [auth A] mmCIF format, chain J [auth A]	B [auth A], J [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain J [auth A] Interactions & Density Focus chain B [auth A] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.273 (Depositor), 0.268 (DCC)
R-Value Work: 0.194 (Depositor), 0.191 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.431	α = 90
b = 43.197	β = 90
c = 50.502	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-05-26

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2009-05-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description