Download MendeleyCrystal structure of hSIRT3 in complex with a specific agonist Amiodarone hydrochloride
Zhang, S., Fu, L., Liu, J., Liu, B.To be published.
5H4D
Crystal structure of hSIRT3 in complex with a specific agonist Amiodarone hydrochloride
- PDB DOI: https://doi.org/10.2210/pdb5H4D/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2016-10-31 Released: 2017-11-08
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.21 Å
- R-Value Free: 0.372
- R-Value Work: 0.213
- R-Value Observed: 0.220
This is version 2.0 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 deacetylase sirtuin-3, mitochondrial | A, C [auth H] | 271 | 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 AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| ARG-HIS-LYS | B [auth D], D [auth C] | 4 | Homo sapiens | Mutation(s): 0 |  |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 6 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAD Query on NAD | H [auth A], O [auth H] | NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N |  | ||
| BBI Query on BBI | G [auth A], N [auth H] | (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone C25 H29 I2 N O3 IYIKLHRQXLHMJQ-UHFFFAOYSA-N |  | ||
| MCM Query on MCM | I [auth D], P [auth C] | 7-AMINO-4-METHYL-CHROMEN-2-ONE C10 H9 N O2 GLNDAGDHSLMOKX-UHFFFAOYSA-N |  | ||
| PEG Query on PEG | J [auth H], L [auth H] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | E [auth A], K [auth H] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| MG Query on MG | F [auth A], M [auth H] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| ALY Query on ALY | B [auth D], D [auth C] | L-PEPTIDE LINKING | C8 H16 N2 O3 |  | LYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.21 Å
- R-Value Free: 0.372
- R-Value Work: 0.213
- R-Value Observed: 0.220
- Space Group: H 3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 114.56 | α = 90 |
| b = 114.56 | β = 90 |
| c = 123.404 | γ = 120 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data collection |
| HKL-2000 | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| MOLREP | phasing |
Entry History
Revision History (Full details and data files)
- Version 1.0: 2017-11-08
Type: Initial release - Version 1.1: 2017-11-22
Changes: Data collection - Version 2.0: 2023-04-05
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
