Download MendeleyInteractions 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
5XHS
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
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.19 Å
- R-Value Free: 0.224
- R-Value Work: 0.173
- R-Value Observed: 0.176
This is version 1.1 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| NAD-dependent protein deacylase sirtuin-5, mitochondrial | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9NXA8 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SLL Query on SLL | C [auth A] | (2S)-2-azanyl-6-[(4-hydroxy-4-oxo-butanoyl)amino]hexanoic acid C10 H18 N2 O5 ZAFOVBXOMIXMTH-ZETCQYMHSA-N |  | ||
| MCM Query on MCM | D [auth A] | 7-AMINO-4-METHYL-CHROMEN-2-ONE C10 H9 N O2 GLNDAGDHSLMOKX-UHFFFAOYSA-N |  | ||
| PHQ Query on PHQ | B [auth A] | benzyl chlorocarbonate C8 H7 Cl O2 HSDAJNMJOMSNEV-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | E [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.19 Å
- R-Value Free: 0.224
- R-Value Work: 0.173
- R-Value Observed: 0.176
- 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 Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
| 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
