Download MendeleySirtuin 2 protein with H3K18 myristoylated peptide
Chen, L.F.To be published.
6L71
Sirtuin 2 demyristoylation native intermediate I & II mixture
- PDB DOI: https://doi.org/10.2210/pdb6L71/pdb
- Classification: TRANSFERASE
- Organism(s): Homo sapiens, synthetic construct
- Expression System: Escherichia coli K-12
- Mutation(s): No
- Deposited: 2019-10-30 Released: 2021-03-31
- Funding Organization(s): The University Grants Committee, Research Grants Council (RGC)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.11 Å
- R-Value Free: 0.224
- R-Value Work: 0.167
- R-Value Observed: 0.170
Starting Model: experimental
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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 deacetylase sirtuin-2 | 304 | Homo sapiens | Mutation(s): 0 Gene Names: SIRT2, SIR2L, SIR2L2 EC: 2.3.1.286 (PDB Primary Data), 2.3.1 (UniProt) |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q8IXJ6 (Homo sapiens) Explore Q8IXJ6 Go to UniProtKB: Q8IXJ6 | |||||
PHAROS: Q8IXJ6 GTEx: ENSG00000068903 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8IXJ6 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| PRO-ARG-LYS-GLN-LEU-ALA | B [auth C] | 6 | synthetic construct | Mutation(s): 0 |  |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| YDD (Subject of Investigation/LOI) Query on YDD | E [auth C] | [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5S)-3,4-bis(oxidanyl)-5-tetradecoxy-oxolan-2-yl]methyl hydrogen phosphate C29 H51 N5 O14 P2 XDVQERDQBQWVRC-UHUMEYFMSA-N |  | ||
| YOY (Subject of Investigation/LOI) Query on YOY | D [auth C] | [[(2S,3aS,5S,6R,6aS)-2-dodecyl-6-oxidanyl-3a,5,6,6a-tetrahydrofuro[2,3-d][1,3]dioxol-5-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate C28 H47 N5 O14 P2 KJBRVZZXXRAVKC-XBVYZWAMSA-N |  | ||
| NCA (Subject of Investigation/LOI) Query on NCA | C [auth A] | NICOTINAMIDE C6 H6 N2 O DFPAKSUCGFBDDF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.11 Å
- R-Value Free: 0.224
- R-Value Work: 0.167
- R-Value Observed: 0.170
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 37.601 | α = 90 |
| b = 78.095 | β = 97.64 |
| c = 56.347 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data scaling |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2021-03-31 Deposition Author(s): Chen, L.F.
| Funding Organization | Location | Grant Number |
|---|---|---|
| The University Grants Committee, Research Grants Council (RGC) | Hong Kong | HKU/C7037-14G |
Revision History (Full details and data files)
- Version 1.0: 2021-03-31
Type: Initial release - Version 1.1: 2023-11-22
Changes: Advisory, Data collection, Database references, Refinement description
