5Y4H | pdb_00005y4h

Human SIRT3 in complex with halistanol sulfate

PDB DOI: https://doi.org/10.2210/pdb5Y4H/pdb

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

Deposited: 2017-08-03 Released: 2018-05-16
Deposition Author(s): Kudo, N., Ito, A., Yoshida, M.
Funding Organization(s): JSPS

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.269 (Depositor), 0.270 (DCC)
R-Value Work:
0.215 (Depositor), 0.220 (DCC)
R-Value Observed:
0.218 (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

Halistanol sulfates I and J, new SIRT1-3 inhibitory steroid sulfates from a marine sponge of the genus Halichondria

Nakamura, F., Kudo, N., Tomachi, Y., Nakata, A., Takemoto, M., Ito, A., Tabei, H., Arai, D., de Voogd, N., Yoshida, M., Nakao, Y., Fusetani, N.

(2018) J Antibiot (Tokyo) 71: 273-278

PubMed: 29184120 Search on PubMed
DOI: https://doi.org/10.1038/ja.2017.145
Primary Citation of Related Structures:
5Y4H

PubMed Abstract:
Two new analogs of halistanol sulfate (1) were isolated from a marine sponge Halichondria sp. collected at Hachijo-jima Island. Structures of these new halistanol sulfates I (2) and J (3) were elucidated by spectral analyses. Compounds 1-3 showed inhibitory activity against SIRT 1-3 with IC ₅₀ ranges of 45.9-67.9, 18.9-21.1 and 21.8-37.5 μM, respectively. X-ray crystallography of the halistanol sulfate (1) and SIRT3 complex clearly indicates that 1 binds to the exosite of SIRT3 that we have discovered in this study.

Organizational Affiliation

Department of Chemistry and Biochemistry, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.

Macromolecule Content

Total Structure Weight: 33.92 kDa
Atom Count: 2,120
Modelled Residue Count: 263
Deposited Residue Count: 297
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-3, mitochondrial	A	285	Homo sapiens	Mutation(s): 0 Gene Names: SIRT3, SIR2L3 EC: 3.5.1 (PDB Primary Data), 2.3.1 (UniProt), 2.3.1.286 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NTG7 (Homo sapiens) Explore Q9NTG7 Go to UniProtKB: Q9NTG7
PHAROS: Q9NTG7 GTEx: ENSG00000142082
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NTG7
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
THr-Arg-Ser-GLY-ALY-VAL-MET-ARG-ARG-LEU-ARG-ARG	B	12	Homo sapiens	Mutation(s): 0 EC: 6.2.1.1 (UniProt), 6.2.1.17 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUB1 (Homo sapiens) Explore Q9NUB1 Go to UniProtKB: Q9NUB1
PHAROS: Q9NUB1 GTEx: ENSG00000154930
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NUB1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8QF Query on 8QF Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	[(2~{S},3~{S},5~{S},6~{S},8~{S},9~{S},10~{R},13~{R},14~{R},17~{R})-17-[(2~{R})-6,6-dimethylheptan-2-yl]-10,13-dimethyl-2,3-disulfooxy-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-6-yl] hydrogen sulfate C₂₈ H₅₀ O₁₂ S₃ MNVNGGMQJFYHMK-NZLCMVQPSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY Query on ALY	B	L-PEPTIDE LINKING	C₈ H₁₆ N₂ O₃		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.269 (Depositor), 0.270 (DCC)
R-Value Work: 0.215 (Depositor), 0.220 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.84	α = 90
b = 127.84	β = 90
c = 127.84	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-05-16

Deposition Author(s):

Kudo, N.

Ito, A.

Yoshida, M.

Funding Organization	Location	Grant Number
JSPS	Japan	KAKENHI 26221204
JSPS	Japan	P-Direct

Revision History (Full details and data files)

Version 1.0: 2018-05-16
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary