4JQL | pdb_00004jql

Synthesis of Benzoquinone-Ansamycin-Inspired Macrocyclic Lactams from Shikimic Acid

PDB DOI: https://doi.org/10.2210/pdb4JQL/pdb

Classification: chaperone/Inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-03-20 Released: 2013-04-10
Deposition Author(s): Jeso, V., Iqbal, S., Hernandez, P., Cameron, M.D., Park, H., Lograsso, P.V., Micalizio, G.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.196 (Depositor), 0.198 (DCC)
R-Value Work:
0.168 (Depositor), 0.171 (DCC)
R-Value Observed:
0.169 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Synthesis of benzoquinone ansamycin-inspired macrocyclic lactams from shikimic Acid.

Jeso, V., Iqbal, S., Hernandez, P., Cameron, M.D., Park, H., Lograsso, P.V., Micalizio, G.C.

(2013) Angew Chem Int Ed Engl 52: 4800-4804

PubMed: 23554224 Search on PubMed
DOI: https://doi.org/10.1002/anie.201301323
Primary Citation Related Structures:
4JQL

Organizational Affiliation

Department of Chemistry, The Scripps Research Institute, 130 Scripps Way #3A2, Jupiter, FL 33458, USA.

Macromolecule Content

Total Structure Weight: 28.55 kDa
Atom Count: 2,031
Modeled Residue Count: 215
Deposited Residue Count: 249
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HSP 90-alpha	A	249	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07900
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VJ6 Query on VJ6 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]	valerjesomycin C₂₈ H₄₁ N₃ O₉ JUJODNDJFVYZOZ-HJVOAZHASA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.196 (Depositor), 0.198 (DCC)
R-Value Work: 0.168 (Depositor), 0.171 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.37	α = 90
b = 44.49	β = 114.8
c = 53.92	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
PHENIX	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: 2013-04-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-04-10
Type: Initial release
Version 1.1: 2013-04-24
Changes: Database references
Version 1.2: 2013-05-22
Changes: Database references
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations