9CBT

Crystal structure of human sirtuin 3 fragment (residues 118-399) bound to intermediates from reaction with NAD and inhibitor NH6-10

PDB DOI: https://doi.org/10.2210/pdb9CBT/pdb

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

Deposited: 2024-06-20 Released: 2024-08-07
Deposition Author(s): Fenwick, M.K., Young, H.J., Lin, H.
Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/Office of the Director, Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.239
R-Value Work: 0.198
R-Value Observed: 0.201

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of human sirtuin 3 fragment (residues 118-399) bound to intermediates from reaction with NAD and inhibitor NH6-10

Fenwick, M.K., Young, J.H., Lin, H.

To be published.

Macromolecule Content

Total Structure Weight: 65.36 kDa
Atom Count: 4,855
Modelled Residue Count: 544
Deposited Residue Count: 564
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-3, mitochondrial	A, B	282	Homo sapiens	Mutation(s): 0 Gene Names: SIRT3 EC: 2.3.1.286
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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5I7 (Subject of Investigation/LOI) Query on 5I7 Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	(phenylmethyl) ~{N}-[(2~{S})-6-[[(2~{R},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-6-oxidanyl-2-tridecyl-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]amino]-1-oxidanylidene-1-[2-(triethyl-$l^{4}-azanyl)ethylamino]hexan-2-yl]carbamate C₅₁ H₈₆ N₉ O₁₆ P₂ S DVXJRXQMZVZLQP-OACJPHNQSA-O		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
5IA (Subject of Investigation/LOI) Query on 5IA 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-{[(2S)-6-[(Z)-(1-{[(2R,3R,4R,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-4-hydroxy-2-sulfanyloxolan-3-yl]oxy}tetradecylidene)amino]-2-{[(benzyloxy)carbonyl]amino}hexanoyl]amino}-N,N,N-triethylethan-1-aminium (non-preferred name) C₅₁ H₈₆ N₉ O₁₆ P₂ S NDEIYVWRFNKRPD-LQYQRRKDSA-O		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PG4 Query on PG4 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]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.239
R-Value Work: 0.198
R-Value Observed: 0.201
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.433	α = 90
b = 63.193	β = 90.79
c = 114.608	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
Coot	model building
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-08-07

Deposition Author(s):

Fenwick, M.K.

Young, H.J.

Lin, H.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK107868-04
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM124165-01
National Institutes of Health/Office of the Director	United States	S10OD021527
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357