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
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 ( ˚ ) |
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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 |