Download Mendeleycomplex structure of histone lysine desuccinylase Sirt5 with succinyl peptide H3K122
Hang, T.R., Chen, W.B., Zang, J.Y., Zhang, X.To be published.
6ACE
histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122
- PDB DOI: https://doi.org/10.2210/pdb6ACE/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2018-07-26 Released: 2019-07-24
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.98 Å
- R-Value Free: 0.266
- R-Value Work: 0.203
- R-Value Observed: 0.206
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.1 of the entry. See complete history.
Literature
To be published.
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 | 267 | Homo sapiens | Mutation(s): 0 Gene Names: SIRT5 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 | |||||
| |||||
Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| succinyl peptide H3K122 | 8 | Homo sapiens | Mutation(s): 0 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q71DI3 (Homo sapiens) Explore Q71DI3 Go to UniProtKB: Q71DI3 | |||||
PHAROS: Q71DI3 | |||||
Entity Groups | |||||
| UniProt Group | Q71DI3 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | D [auth A], E [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | C [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| SLL Query on SLL | B | L-PEPTIDE LINKING | C10 H18 N2 O5 |  | LYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.98 Å
- R-Value Free: 0.266
- R-Value Work: 0.203
- R-Value Observed: 0.206
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 123.227 | α = 90 |
| b = 41.169 | β = 94.69 |
| c = 55.854 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2019-07-24 Deposition Author(s): Hang, T.R., Chen, W.B.
| Funding Organization | Location | Grant Number |
|---|---|---|
| China | 2017YFA0503600 | |
| China | 2016YFA0400903 | |
| China | XDB19000000 | |
| China | 31621002 | |
| China | U1532109 | |
| China | 31700671 | |
| China | 2017FXCX004 | |
| China | 1608085QC52 |
Revision History (Full details and data files)
- Version 1.0: 2019-07-24
Type: Initial release - Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description
