Download Mendeleycomplex structure of histone lysine desuccinylase Sirt5 with succinyl peptide H2BK120
Hang, T.R., Chen, W.B.To be published.
6ACO
histone lysine desuccinylase Sirt5 in complex with succinyl peptide H2BK120
- PDB DOI: https://doi.org/10.2210/pdb6ACO/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: 1.71 Å
- R-Value Free: 0.217
- R-Value Work: 0.161
- R-Value Observed: 0.164
Starting Model: experimental
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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 | 270 | 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 H2BK120 | 7 | Homo sapiens | Mutation(s): 0 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P62807 (Homo sapiens) Explore P62807 Go to UniProtKB: P62807 | |||||
PHAROS: P62807 | |||||
Entity Groups | |||||
| UniProt Group | P62807 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | E [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | C [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| CL Query on CL | D [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| 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: 1.71 Å
- R-Value Free: 0.217
- R-Value Work: 0.161
- R-Value Observed: 0.164
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 33.885 | α = 90 |
| b = 64.877 | β = 95.92 |
| c = 55.564 | 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
