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233,605 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Structure Author = "Julien, S."

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Search Summary

This query matches 32 Structures.

Refinements

Structure Determination Methodology

experimental (32)

Scientific Name of Source Organism

	Homo sapiens (30)
	Danio rerio (6)
	synthetic construct (4)

Taxonomy

	Eukaryota (32)
	other sequences (4)
	Eukaryota (eukaryotes) (2)

Experimental Method

X-RAY DIFFRACTION (32)

Polymer Entity Type

Protein (32)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (15)
	2.0 - 2.5 (8)
	2.5 - 3.0 (4)
	3.0 - 3.5 (2)

Release Date

	2005 - 2009 (2)
	2010 - 2014 (6)
	2015 - 2019 (13)
	2020 - 2024 (11)

Enzyme Classification Name

	Transferases (32)
	Hydrolases (21)
	Oxidoreductases (5)
	Ligases (1)

Symmetry Type

	Asymmetric (32)
	Cyclic (2)

SCOP Classification

	Alpha and beta proteins (a/b) (8)
	Artifacts (4)

AllSelected

1 to 25 of 32 Structures

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2B4Y \| pdb_00002b4y	Download File View File

Crystal Structure of Human Sirtuin homolog 5

Min, J.R., Antoshenko, T., Dong, A., Schuetz, A., Loppnau, P., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

To be published

Released	2006-02-28
Method	X-RAY DIFFRACTION 1.9 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent deacetylase sirtuin-5 (protein)
Unique Ligands	APR, EPE, ZN

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2NYR \| pdb_00002nyr	Download File View File

Crystal Structure of Human Sirtuin Homolog 5 in Complex with Suramin

Min, J.R., Antoshenko, T., Allali-Hassani, A., Dong, A., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

(2007) Structure 15: 377-389

Released	2006-12-19
Method	X-RAY DIFFRACTION 2.06 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent deacetylase sirtuin-5 (protein)
Unique Ligands	SVR, ZN

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3RIG \| pdb_00003rig	Download File View File

Sirt5 is an NAD-dependent protein lysine demalonylase and desuccinylase

Zhou, Y.

(2011) Science 334: 806-809

Released	2011-11-23
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent deacetylase sirtuin-5 (protein) peptide of histone 3 thioacetyl-lysine 9 (protein)
Unique Ligands	NHE, ZN

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3RIY \| pdb_00003riy	Download File View File

Sirt5 is an NAD-dependent protein lysine demalonylase and desuccinylase

Zhou, Y., Hao, Q.

(2011) Science 334: 806-809

Released	2011-11-23
Method	X-RAY DIFFRACTION 1.55 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent deacetylase sirtuin-5 (protein) peptide of histone 3 N-succinyl lysine 9 (protein)
Unique Ligands	NAD, ZN

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4F4U \| pdb_00004f4u	Download File View File

The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5

Zhou, Y., Hao, Q.

(2012) J Biological Chem 287: 28307-28314

Released	2012-06-20
Method	X-RAY DIFFRACTION 2 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent lysine demalonylase and desuccinylase sirtuin-5, mitochondrial (protein) peptide from Histone H3.1 (protein)
Unique Ligands	ZN

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4F56 \| pdb_00004f56	Download File View File

The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5

Zhou, Y., Hao, Q.

(2012) J Biological Chem 287: 28307-28314

Released	2012-06-20
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent lysine demalonylase and desuccinylase sirtuin-5, mitochondrial (protein) peptide from Histone H3.1 (protein)
Unique Ligands	CGK, ZN

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4G1C \| pdb_00004g1c	Download File View File

Human SIRT5 bound to Succ-IDH2 and Carba-NAD

Dai, H.

(2012) J Org Chem 77: 7319-7329

Released	2012-08-15
Method	X-RAY DIFFRACTION 1.944 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent protein deacylase sirtuin-5, mitochondrial (protein) Succinylated IDH2 peptide (protein)
Unique Ligands	CNA, ZN

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4HDA \| pdb_00004hda	Download File View File

Crystal structure of human Sirt5 in complex with Fluor-de-Lys peptide and resveratrol

Gertz, M., Steegborn, C.

(2012) PLoS One 7: e49761-e49761

Released	2012-12-05
Method	X-RAY DIFFRACTION 2.601 Å
Organisms	Homo sapiens
Macromolecule	Fluor-de-Lys peptide (protein) NAD-dependent protein deacylase sirtuin-5, mitochondrial (protein)
Unique Ligands	STL, ZN

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5BWL \| pdb_00005bwl	Download File View File

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

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

To be published

Released	2016-07-13
Method	X-RAY DIFFRACTION 1.548 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	Coumarin-labelled succinyl peptide (protein) NAD-dependent protein deacylase sirtuin-5, mitochondrial (protein)
Unique Ligands	MCM, ZN

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5OJO \| pdb_00005ojo	Download File View File

Sirtuin 5 from Danio rerio in complex with 3-hydroxy-3-methylglutaryl-CPS1 peptide

Pannek, M., Steegborn, C.

(2017) Nat Commun 8: 1513-1513

Released	2017-11-29
Method	X-RAY DIFFRACTION 3.1 Å
Organisms	Danio rerio Homo sapiens
Macromolecule	Carbamoyl-phosphate synthase [ammonia], mitochondrial (protein) NAD-dependent protein deacylase sirtuin-5, mitochondrial (protein)
Unique Ligands	DMS, EDO, EPE, NA, ZN

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5XHS \| pdb_00005xhs	Download File View File

Crystal structure of SIRT5 complexed with a fluorogenic small-molecule substrate SuBKA

Yu, Y., Li, B., Chen, Q.

(2017) RSC Adv 7: 36214-36222

Released	2018-05-02
Method	X-RAY DIFFRACTION 2.19 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent protein deacylase sirtuin-5, mitochondrial (protein)
Unique Ligands	MCM, PHQ, SLL, ZN

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6ACE \| pdb_00006ace	Download File View File

histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122

Hang, T.R., Chen, W.B.

To be published

Released	2019-07-24
Method	X-RAY DIFFRACTION 1.98 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent protein deacylase sirtuin-5, mitochondrial (protein) succinyl peptide H3K122 (protein)
Unique Ligands	GOL, ZN

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6ACL \| pdb_00006acl	Download File View File

histone lysine desuccinylase Sirt5 in complex with succinyl peptide H2AK95

Hang, T.R., Chen, W.B.

To be published

Released	2019-07-24
Method	X-RAY DIFFRACTION 1.92 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent protein deacylase sirtuin-5, mitochondrial (protein) succinyl peptide H2AK95 (protein)
Unique Ligands	ZN

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6ACO \| pdb_00006aco	Download File View File

histone lysine desuccinylase Sirt5 in complex with succinyl peptide H2BK120

Hang, T.R., Chen, W.B.

To be published

Released	2019-07-24
Method	X-RAY DIFFRACTION 1.71 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent protein deacylase sirtuin-5, mitochondrial (protein) succinyl peptide H2BK120 (protein)
Unique Ligands	CL, GOL, ZN

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6ACP \| pdb_00006acp	Download File View File

histone lysine desuccinylase Sirt5 in complex with succinyl peptide H4K91

Hang, T.R., Chen, W.B.

To be published

Released	2019-07-24
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent protein deacylase sirtuin-5, mitochondrial (protein) succinyl peptide H4K91 (protein)
Unique Ligands	ZN

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6ENX \| pdb_00006enx	Download File View File

Zebrafish Sirt5 in complex with stalled bicyclic intermediate of inhibitory compound 10

Pannek, M., Steegborn, C.

(2017) Angew Chem Int Ed Engl 56: 14836-14841

Released	2017-11-01
Method	X-RAY DIFFRACTION 1.95 Å
Organisms	Danio rerio
Macromolecule	NAD-dependent protein deacylase sirtuin-5, mitochondrial (protein)
Unique Ligands	BJW, DMS, ZN

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6EO0 \| pdb_00006eo0	Download File View File

Zebrafish Sirt5 in complex with stalled peptidylimidate and bicyclic intermediate of inhibitory compound 29

Pannek, M., Steegborn, C.

(2017) Angew Chem Int Ed Engl 56: 14836-14841

Released	2017-11-01
Method	X-RAY DIFFRACTION 2.4 Å
Organisms	Danio rerio
Macromolecule	NAD-dependent protein deacylase sirtuin-5, mitochondrial (protein)
Unique Ligands	BV8, BVT, EDO, ZN

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6EQS \| pdb_00006eqs	Download File View File

Human Sirt5 in complex with stalled peptidylimidate intermediate of inhibitory compound 29

Pannek, M., Steegborn, C.

(2017) Angew Chem Int Ed Engl 56: 14836-14841

Released	2017-11-01
Method	X-RAY DIFFRACTION 1.32 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent protein deacylase sirtuin-5, mitochondrial (protein)
Unique Ligands	BU2, BV8, DMS, EDO, ZN

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6FKY \| pdb_00006fky	Download File View File

Crystal structure of zebrafish Sirtuin 5 in complex with 3-(benzylthio)succinyl-CPS1 peptide

Pannek, M., Steegborn, C.

(2018) J Med Chem 61: 2460-2471

Released	2018-03-21
Method	X-RAY DIFFRACTION 2.98 Å
Organisms	Danio rerio Homo sapiens
Macromolecule	3(R)-(phenylthio)succinyl-CPS1 peptide (protein) NAD-dependent protein deacylase sirtuin-5, mitochondrial (protein)
Unique Ligands	DZK, E9N, EDO, EPE, NA, ZN

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6FKZ \| pdb_00006fkz	Download File View File

Crystal structure of zebrafish Sirtuin 5 in complex with 3-(phenylthio)succinyl-CPS1 peptide

Pannek, M., Steegborn, C.

(2018) J Med Chem 61: 2460-2471

Released	2018-05-16
Method	X-RAY DIFFRACTION 3.3 Å
Organisms	Danio rerio Homo sapiens
Macromolecule	3(R)-(phenylthio)succinyl-CPS1 peptide (protein) 3(S)-(phenylthio)succinyl-CPS1 peptide (protein) NAD-dependent protein deacylase sirtuin-5, mitochondrial (protein)
Unique Ligands	EPE, GOL, ZN

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6FLG \| pdb_00006flg	Download File View File

Crystal structure of zebrafish Sirtuin 5 in complex with 3(S)-(naphthylthio)succinyl-CPS1 peptide

Pannek, M., Steegborn, C.

(2018) J Med Chem 61: 2460-2471

Released	2018-04-18
Method	X-RAY DIFFRACTION 2.5 Å
Organisms	Danio rerio Homo sapiens
Macromolecule	3(S)-(naphthylthio)succinyl-CPS1 peptide (protein) NAD-dependent protein deacylase sirtuin-5, mitochondrial (protein)
Unique Ligands	DMS, EDO, EPE, ZN

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6LJK \| pdb_00006ljk	Download File View File

Crystal structure of human Sirt5 in complex with an internally quenched fluorescent substrate GluIQF

Chen, Q., Yu, Y.

(2020) Eur J Med Chem 192: 112201-112201

Released	2020-12-23
Method	X-RAY DIFFRACTION 1.394 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	BE2-SER-ALA-ILE-LYS-SER-NIY-GLY-SET (protein) NAD-dependent protein deacylase sirtuin-5, mitochondrial (protein)
Unique Ligands	GUA, NA, ZN

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6LJM \| pdb_00006ljm	Download File View File

Crystal structure of human Sirt5 in complex with the fluorogenic tetrapeptide substrate P13

Chen, Q., Yu, Y.

(2020) Eur J Med Chem 192: 112201-112201

Released	2020-10-28
Method	X-RAY DIFFRACTION 1.78 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	ACE-SER-LEU-GLY-SLL (protein) NAD-dependent protein deacylase sirtuin-5, mitochondrial (protein)
Unique Ligands	MCM, ZN

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6LJN \| pdb_00006ljn	Download File View File

Crystal structure of human Sirt5 in complex with the fluorogenic tetrapeptide substrate P15

Chen, Q., Yu, Y.

(2020) Eur J Med Chem 192: 112201-112201

Released	2020-10-28
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	ACE-HIS-PHE-SER-SLL (protein) NAD-dependent protein deacylase sirtuin-5, mitochondrial (protein)
Unique Ligands	MCM, ZN

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7X3P \| pdb_00007x3p	Download File View File

Crystal structure of human SIRT5 in complex with diazirine inhibitor 9

Li, G.-B., Deng, J.

To be published

Released	2023-09-06
Method	X-RAY DIFFRACTION 1.56 Å
Organisms	Homo sapiens
Macromolecule	NAD-dependent protein deacylase sirtuin-5, mitochondrial (protein)
Unique Ligands	8VG, PEG, ZN

1 to 25 of 32 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

2B4Y | pdb_00002b4y

2NYR | pdb_00002nyr

3RIG | pdb_00003rig

3RIY | pdb_00003riy

4F4U | pdb_00004f4u

4F56 | pdb_00004f56

4G1C | pdb_00004g1c

4HDA | pdb_00004hda

5BWL | pdb_00005bwl

5OJO | pdb_00005ojo

5XHS | pdb_00005xhs

6ACE | pdb_00006ace

6ACL | pdb_00006acl

6ACO | pdb_00006aco

6ACP | pdb_00006acp

6ENX | pdb_00006enx

6EO0 | pdb_00006eo0

6EQS | pdb_00006eqs

6FKY | pdb_00006fky

6FKZ | pdb_00006fkz

6FLG | pdb_00006flg

6LJK | pdb_00006ljk

6LJM | pdb_00006ljm

6LJN | pdb_00006ljn

7X3P | pdb_00007x3p