4F56: PDB entry 4F56

The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5. Determined by X-ray diffraction at 1.7 Å resolution. Released 20 Jun 2012.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,785
Mol. weight: 63.3 kDa
Ligands: ZN, CGK
Released: 20 Jun 2012

Explore 4F56 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4F56 contains 37 α-helices and 36 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	37	1	1
α-helix	40-49	10
β-strand	52-57	6	1
α-helix	59-61	3
α-helix	63-65	3
β-strand	77	1	2
β-strand	80	1	2
α-helix	82-85	4
α-helix	88-93	6
α-helix	95-110	16
α-helix	116-130	15
β-strand	134-139	6	1
α-helix	145-149	5
β-strand	154-156	3	1
β-strand	159-166	8	3
β-strand	172-174	3	3
α-helix	182-184	3
α-helix	194-196	3
α-helix	201-203	3
β-strand	206	1	4
α-helix	214	1
β-strand	215	1	4
β-strand	216-220	5	3
α-helix	221-222	2
β-strand	226	1	5
α-helix	227-228	2
α-helix	229-241	13
β-strand	244-248	5	1
β-strand	255	1	6
α-helix	257-259	3
α-helix	260-266	7
β-strand	271-275	5	1
α-helix	282-284	3
β-strand	287-290	4	1
α-helix	293-301	9

Chain B: 18 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	37	1	7
α-helix	40-49	10
β-strand	52-57	6	7
α-helix	59-61	3
α-helix	63-65	3
β-strand	77	1	8
β-strand	80	1	8
α-helix	82-85	4
α-helix	88-93	6
α-helix	95-109	15
α-helix	116-129	14
β-strand	134-139	6	7
α-helix	145-149	5
β-strand	154-156	3	7
β-strand	159-166	8	9
β-strand	172-174	3	9
α-helix	182-184	3
α-helix	201-203	3
β-strand	206	1	10
α-helix	214	1
β-strand	215	1	10
β-strand	216-220	5	9
α-helix	221-222	2
β-strand	226	1	11
α-helix	227-228	2
α-helix	229-241	13
β-strand	244-248	5	7
β-strand	255	1	12
α-helix	257-259	3
α-helix	260-266	7
β-strand	271-275	5	7
α-helix	282-284	3
β-strand	287-290	4	7
α-helix	293-300	8

Chains C and D: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	5
β-strand	10	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent lysine demalonylase and desuccinylase sirtuin-5, mitochondrial	A, B	protein	273	Homo sapiens	Q9NXA8 (AlphaFold model)
peptide from Histone H3.1	C, D	protein	12	Homo sapiens	P68431 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4F56_1 NAD-dependent lysine demalonylase and desuccinylase sirtuin-5, mitochondrial (chains A, B)
GSFTARPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPL
AFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKA
GTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEE
AGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGV
PVAEFNTETTPATNRFRFHFQGPCGTTLPEALA

Sequence of entity 2 (C, D), FASTA

>4F56_2 peptide from Histone H3.1 (chains C, D)
KQTARKSTGGKA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
CGK	3-[(2R,3aR,5R,6R,6aR)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-…	C19 H27 N5 O16 P2 S	2

Primary citation

The Bicyclic Intermediate Structure Provides Insights into the Desuccinylation Mechanism of Human Sirtuin 5 (SIRT5). Zhou, Y., Zhang, H., He, B. et al. J Biol Chem (2012) 287:28307-28314. DOI 10.1074/jbc.M112.384511 · PubMed

Other PDB entries of the same protein (UniProt Q9NXA8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6EQS 1.32 Å, Human Sirt5 in complex with stalled peptidylimidate intermediate of inhibitory compound 29
6LJK 1.39 Å, Crystal structure of human Sirt5 in complex with an internally quenched fluorescent…
8Z54 1.45 Å, Crystal structure of human SIRT5 in complex with succinylated Prx1 fragment
5BWL 1.55 Å, Crystal Structure of SIRT5 in Complex with a Coumarin-Labelled Succinyl Peptide
3RIY 1.55 Å, Sirt5 is an NAD-dependent protein lysine demalonylase and desuccinylase
7X3P 1.56 Å, Crystal structure of human SIRT5 in complex with diazirine inhibitor 9
9V0H 1.67 Å, Crystal structure of human SIRT5 in complex with inhibitor 0904
6ACO 1.71 Å, histone lysine desuccinylase Sirt5 in complex with succinyl peptide H2BK120
6LJM 1.78 Å, Crystal structure of human Sirt5 in complex with the fluorogenic tetrapeptide substrate…
6LJN 1.8 Å, Crystal structure of human Sirt5 in complex with the fluorogenic tetrapeptide substrate…
8Z56 1.81 Å, Crystal structure of human Q140L-SIRT5 in complex with succinylated Prx1 fragment
8Z55 1.83 Å, Crystal structure of human SIRT5 in complex with succPrx1 and ADP ribose

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