5BWL

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.236
R-Value Work: 0.212
R-Value Observed: 0.213

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

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

Gai, W., Jiang, H., Liu, D.

To be published.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
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 Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coumarin-labelled succinyl peptide	B	3	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MCM Query on MCM Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B]	D [auth B]	7-AMINO-4-METHYL-CHROMEN-2-ONE C₁₀ H₉ N O₂ GLNDAGDHSLMOKX-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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: 1.55 Å
R-Value Free: 0.236
R-Value Work: 0.212
R-Value Observed: 0.213
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-07-13

Deposition Author(s):

Gai, W.

Jiang, H.

Liu, D.

Revision History (Full details and data files)

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

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Help and Resources

5BWL

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)