5BWL | pdb_00005bwl

Crystal Structure of SIRT5 in Complex with a Coumarin-Labelled Succinyl Peptide

• PDB DOI: https://doi.org/10.2210/pdb5BWL/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-06-08 Released: 2016-07-13 
• Deposition Author(s): Gai, W., Jiang, H., Liu, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.236 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of SIRT5 in Complex with a Coumarin-Labelled Succinyl Peptide

Gai, W., Jiang, H., Liu, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.24 kDa 
• Atom Count: 2,459 
• Modeled Residue Count: 270 
• Deposited Residue Count: 293 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacylase sirtuin-5, mitochondrial	A	290	Homo sapiens	Mutation(s): 0  Gene Names: SIRT5, SIR2L5 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coumarin-labelled succinyl peptide	B	3	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MCM	D [auth B]	7-AMINO-4-METHYL-CHROMEN-2-ONE C10 H9 N O2 GLNDAGDHSLMOKX-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SLL	B	L-PEPTIDE LINKING	C10 H18 N2 O5		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.236 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.42	α = 90
b = 55.536	β = 90
c = 124.68	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHENIX	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-13 
Deposition Author(s): Gai, W., Jiang, H., Liu, D.

Revision History  

• Version 1.0: 2016-07-13
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description