4BV2: SIR2

Crystal structure of SIR2 in complex with the inhibitor ex-527, 2'-O-acetyl-ADP-ribose and deacetylated P53-peptide. Determined by X-ray diffraction at 3.3 Å resolution. Released 17 Jul 2013.

Method: X-ray diffraction
Resolution: 3.3 Å
Organisms: THERMOTOGA MARITIMA, HOMO SAPIENS
Chains: 4
Atoms: 3,853
Mol. weight: 60.17 kDa
Ligands: ZN, OCZ, OAD
Released: 17 Jul 2013

Explore 4BV2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4BV2 contains 32 α-helices and 32 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: 16 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	4-12	9
β-strand	16-20	5	1
α-helix	22-24	3
α-helix	26-28	3
β-strand	49	1	2
α-helix	50-55	6
α-helix	57-67	11
α-helix	69-73	5
α-helix	78-88	11
β-strand	94-97	4	1
α-helix	103-106	4
β-strand	112-114	3	1
β-strand	117-124	8	3
β-strand	130-132	3	3
α-helix	133-139	7
β-strand	147	1	4
α-helix	153	1
β-strand	154	1	4
β-strand	155-159	5	3
β-strand	162	1	2
β-strand	165	1	5
α-helix	166-167	2
α-helix	168-180	13
β-strand	183-187	5	1
β-strand	194	1	6
α-helix	196-198	3
α-helix	199-206	8
β-strand	209-213	5	1
α-helix	221-223	3
β-strand	226-228	3	1
α-helix	232-243	12

Chain B: 16 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	4-12	9
β-strand	16-20	5	7
α-helix	22-24	3
α-helix	26-28	3
β-strand	49	1	8
α-helix	50-55	6
α-helix	57-67	11
α-helix	69-73	5
α-helix	78-88	11
β-strand	94-97	4	7
α-helix	103-106	4
β-strand	112-114	3	7
β-strand	117-124	8	9
β-strand	130-132	3	9
α-helix	133-139	7
β-strand	147	1	10
α-helix	153	1
β-strand	154	1	10
β-strand	155-159	5	9
β-strand	162	1	8
β-strand	165	1	11
α-helix	166-167	2
α-helix	168-180	13
β-strand	183-187	5	7
α-helix	196-198	3
α-helix	199-206	8
β-strand	209-213	5	7
α-helix	221-223	3
β-strand	226-228	3	7
α-helix	232-243	12

Chain E: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	5
β-strand	4	1	6

Chain H: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent protein deacetylase	A, B	protein	246	THERMOTOGA MARITIMA	Q9WYW0 (AlphaFold model)
Cellular tumor antigen P53	E, H	protein	13	HOMO SAPIENS	P04637 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4BV2_1 NAD-DEPENDENT PROTEIN DEACETYLASE (chains A, B)
MKMKEFLDLLNESRLTVTLTGAGISTPSGIPDFRGPNGIYKKYSQNVFDIDFFYSHPEEF
YRFAKEGIFPMLQAKPNLAHVLLAKLEEKGLIEAVITQNIDRLHQRAGSKKVIELHGNVE
EYYCVRCEKKYTVEDVIKKLESSDVPLCDDCNSLIRPNIVFFGENLPQDALREAIGLSSR
ASLMIVLGSSLVVYPAAELPLITVRSGGKLVIVNLGETPFDDIATLKYNMDVVEFARRVM
EEGGIS

Sequence of entity 2 (E, H), FASTA

>4BV2_2 CELLULAR TUMOR ANTIGEN P53 (chains E, H)
STSRHKKLMFKTE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
OCZ	(1S)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1- carboxamide	C13 H13 Cl N2 O	2
OAD	2'-O-acetyl adenosine-5-diphosphoribose	C17 H25 N5 O15 P2	2

Primary citation

Ex-527 Inhibits Sirtuins by Exploiting Their Unique Nad+-Dependent Deacetylation Mechanism. Gertz, M., Fischer, F., Nguyen, G.T.T. et al. Proc Natl Acad Sci U S A (2013) 110:E2772. DOI 10.1073/PNAS.1303628110 · PubMed

Other PDB entries of the same protein (UniProt Q9WYW0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1YC5 1.4 Å, Sir2-p53 peptide-nicotinamide
3JR3 1.5 Å, Sir2 bound to acetylated peptide
2H2G 1.63 Å, The Structural Basis of Sirtuin substrate affinity
2H2D 1.7 Å, The Structural Basis for Sirtuin Substrate Affinity
2H2I 1.8 Å, The Structural basis of Sirtuin Substrate Affinity
3PDH 1.8 Å, Structure of Sir2Tm bound to a propionylated peptide
2H59 1.9 Å, Sir2 H116A-deacetylated p53 peptide-3'-o-acetyl ADP ribose
3D4B 1.9 Å, Crystal structure of Sir2Tm in complex with Acetyl p53 peptide and DADMe-NAD+
4BUZ 1.9 Å, SIR2 complex structure mixture of ex-527 inhibitor and reaction products or of reaction…
2H4H 1.99 Å, Sir2 H116Y mutant-p53 peptide-NAD
2H4F 2.0 Å, Sir2-p53 peptide-NAD+
2H4J 2.1 Å, Sir2-deacetylated peptide (from enzymatic turnover in crystal)

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