Download MendeleyCrystal Structure of SIRT3 in complex with H3K4bhb peptide
Zhang, X., Li, H.To be published.
5Z94
Crystal Structure of SIRT3 in complex with H3K4bhb peptide
- PDB DOI: 10.2210/pdb5Z94/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2018-02-02 Released: 2019-02-06
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.191
- R-Value Work: 0.161
- R-Value Observed: 0.162
wwPDB Validation 3D Report Full Report
This is version 1.0 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, B | 283 | Homo sapiens | Mutation(s): 0 Gene Names: SIRT3, SIR2L3 EC: 3.5.1 (PDB Primary Data), 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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9NTG7 | ||||
Protein Feature ViewExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Gene for histone H3 (germline gene) | C, D | 15 | Homo sapiens | Mutation(s): 0 |  |
UniProt | |||||
Find proteins for V9H1G0 (Homo sapiens) Explore V9H1G0 Go to UniProtKB: V9H1G0 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | V9H1G0 | ||||
Protein Feature ViewExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CIT Query on CIT | I [auth A], M [auth B] | CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N |  | Ligand Interaction | |
| SO4 Query on SO4 | H [auth A], L [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | Ligand Interaction | |
| GOL Query on GOL | F [auth A], G [auth A], K [auth B], N [auth D] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | Ligand Interaction | |
| ZN Query on ZN | E [auth A], J [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | Ligand Interaction | |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| KHB Query on KHB | C, D | L-PEPTIDE LINKING | C10 H20 N2 O4 |  | LYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.191
- R-Value Work: 0.161
- R-Value Observed: 0.162
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 75.472 | α = 90 |
| b = 76.26 | β = 115.77 |
| c = 75.425 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| MOLREP | phasing |
Entry History
Revision History (Full details and data files)
- Version 1.0: 2019-02-06
Type: Initial release
