5XHS | pdb_00005xhs

Crystal structure of SIRT5 complexed with a fluorogenic small-molecule substrate SuBKA

PDB DOI: https://doi.org/10.2210/pdb5XHS/pdb

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

Deposited: 2017-04-24 Released: 2018-05-02
Deposition Author(s): Yu, Y., Li, B., Chen, Q.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.224 (Depositor), 0.229 (DCC)
R-Value Work:
0.173 (Depositor), 0.179 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5XHS

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Interactions between sirtuins and fluorogenic small-molecule substrates offer insights into inhibitor design

Wang, H.L., Liu, S., Yu, Z.J., Wu, C., Cheng, L., Wang, Y., Chen, K., Zhou, S., Chen, Q., Yu, Y., Li, G.B.

(2017) RSC Adv 7: 36214-36222

DOI: https://doi.org/10.1039/C7RA05824A

Macromolecule Content

Total Structure Weight: 32.11 kDa
Atom Count: 2,182
Modeled Residue Count: 262
Deposited Residue Count: 288
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacylase sirtuin-5, mitochondrial	A	288	Homo sapiens	Mutation(s): 0 Gene Names: SIRT5, SIR2L5 EC: 3.5.1 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXA8 (Homo sapiens) Explore Q9NXA8 Go to UniProtKB: Q9NXA8
PHAROS: Q9NXA8 GTEx: ENSG00000124523
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NXA8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SLL Query on SLL 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]	(2S)-2-azanyl-6-[(4-hydroxy-4-oxo-butanoyl)amino]hexanoic acid C₁₀ H₁₈ N₂ O₅ ZAFOVBXOMIXMTH-ZETCQYMHSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MCM Query on MCM 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]	7-AMINO-4-METHYL-CHROMEN-2-ONE C₁₀ H₉ N O₂ GLNDAGDHSLMOKX-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PHQ Query on PHQ 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]	benzyl chlorocarbonate C₈ H₇ Cl O₂ HSDAJNMJOMSNEV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.224 (Depositor), 0.229 (DCC)
R-Value Work: 0.173 (Depositor), 0.179 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.13	α = 90
b = 55.274	β = 90
c = 124.303	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-05-02

Deposition Author(s):

Funding Organization	Location	Grant Number
	China	--

Revision History (Full details and data files)

Version 1.0: 2018-05-02
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.