complex structure of histone lysine desuccinylase Sirt5 with succinyl peptide H3K122
Hang, T.R., Chen, W.B., Zang, J.Y., Zhang, X.To be published.
Experimental Data Snapshot
Starting Model: experimental
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wwPDB Validation   3D Report Full Report
Entity ID: 1 | |||||
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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 | ![]() | |
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 | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
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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 GTEx:  ENSG00000183598  | |||||
Entity Groups   | |||||
UniProt Group | Q71DI3 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 2 Unique | |||||
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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 | |||||
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ID | Chains | Type | Formula | 2D Diagram | Parent |
SLL Query on SLL | B | L-PEPTIDE LINKING | C10 H18 N2 O5 | LYS |
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 123.227 | α = 90 |
b = 41.169 | β = 94.69 |
c = 55.854 | γ = 90 |
Software Name | Purpose |
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REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
Funding Organization | Location | Grant Number |
---|---|---|
China | 2017YFA0503600 | |
China | 2016YFA0400903 | |
China | XDB19000000 | |
China | 31621002 | |
China | U1532109 | |
China | 31700671 | |
China | 2017FXCX004 | |
China | 1608085QC52 |