1YC2: Sir2Af2-NAD-ADPribose-nicotinamide

Sir2Af2-NAD-ADPribose-nicotinamide. Determined by X-ray diffraction at 2.4 Å resolution. Released 29 Mar 2005.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Archaeoglobus fulgidus
Chains: 5
Atoms: 10,409
Mol. weight: 149.54 kDa
Ligands: ZN, NAD, NCA, 2PE
Released: 29 Mar 2005

Explore 1YC2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1YC2 contains 78 α-helices and 55 β-strands across 5 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: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
β-strand	18-22	5	1
α-helix	24-30	7
α-helix	38-44	7
α-helix	47-51	5
β-strand	52	1	2
α-helix	53-58	6
α-helix	60-70	11
α-helix	80-90	11
β-strand	94-99	6	1
α-helix	105-108	4
β-strand	114-116	3	1
β-strand	119-126	8	3
β-strand	132-134	3	3
α-helix	135-137	3
α-helix	139-143	5
α-helix	146-148	3
β-strand	158-162	5	3
β-strand	165	1	2
α-helix	171-183	13
β-strand	186-190	5	1
α-helix	202-209	8
β-strand	212-217	6	1
α-helix	224-226	3
β-strand	229-232	4	1
α-helix	235-250	16

Chain B: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-13	11
β-strand	18-22	5	4
α-helix	24-30	7
α-helix	37-42	6
α-helix	47-50	4
β-strand	52	1	5
α-helix	53-58	6
α-helix	60-67	8
α-helix	80-90	11
β-strand	94-99	6	4
α-helix	105-108	4
β-strand	114-116	3	4
β-strand	119-126	8	6
β-strand	132-134	3	6
α-helix	135-138	4
α-helix	139-143	5
α-helix	146-148	3
β-strand	158-162	5	6
β-strand	165	1	5
α-helix	171-183	13
β-strand	186-190	5	4
α-helix	202-208	7
β-strand	212-217	6	4
α-helix	224-226	3
β-strand	229-232	4	4
α-helix	235-250	16

Chain C: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	2-13	12
β-strand	18-22	5	7
α-helix	24-30	7
α-helix	37-42	6
α-helix	47-50	4
β-strand	52	1	8
α-helix	53-58	6
α-helix	60-68	9
α-helix	80-90	11
β-strand	94-99	6	7
α-helix	105-108	4
β-strand	114-116	3	7
β-strand	119-126	8	9
β-strand	132-134	3	9
α-helix	135-138	4
α-helix	139-143	5
β-strand	158-162	5	9
α-helix	163-164	2
β-strand	165	1	8
α-helix	171-183	13
β-strand	186-190	5	7
α-helix	202-208	7
β-strand	212-217	6	7
α-helix	224-226	3
β-strand	229-232	4	7
α-helix	235-251	17

Chain D: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	3-14	12
β-strand	18-22	5	10
α-helix	26-29	4
α-helix	38-44	7
α-helix	47-50	4
β-strand	52	1	11
α-helix	53-58	6
α-helix	60-69	10
α-helix	80-90	11
β-strand	94-99	6	10
α-helix	105-108	4
β-strand	114-116	3	10
β-strand	119-126	8	12
β-strand	132-134	3	12
α-helix	135-137	3
α-helix	139-143	5
α-helix	146-148	3
β-strand	158-162	5	12
α-helix	163-164	2
β-strand	165	1	11
α-helix	171-183	13
β-strand	186-190	5	10
α-helix	202-208	7
β-strand	212-217	6	10
α-helix	224-226	3
β-strand	229-232	4	10
α-helix	235-250	16

Chain E: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	2-13	12
β-strand	18-22	5	13
α-helix	24-30	7
α-helix	32-34	3
α-helix	41-44	4
α-helix	47-50	4
β-strand	52	1	14
α-helix	53-58	6
α-helix	60-69	10
α-helix	80-90	11
β-strand	94-99	6	13
α-helix	105-109	5
β-strand	114-116	3	13
β-strand	119-126	8	15
β-strand	132-134	3	15
α-helix	135-137	3
α-helix	139-142	4
α-helix	146-148	3
β-strand	158-162	5	15
β-strand	165	1	14
α-helix	168-170	3
α-helix	171-182	12
β-strand	186-190	5	13
α-helix	201-209	9
β-strand	212-216	5	13
α-helix	224-226	3
β-strand	229-231	3	13
α-helix	235-249	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent deacetylase 2	A, B, C, D, E	protein	253	Archaeoglobus fulgidus	O30124 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E), FASTA

>1YC2_1 NAD-dependent deacetylase 2 (chains A, B, C, D, E)
MEDEIRKAAEILAKSKHAVVFTGAGISAESGIPTFRGEDGLWRKYDPEEVASISGFKRNP
RAFWEFSMEMKDKLFAEPNPAHYAIAELERMGIVKAVITQNIDMLHQRAGSRRVLELHGS
MDKLDCLDCHETYDWSEFVEDFNKGEIPRCRKCGSYYVKPRVVLFGEPLPQRTLFEAIEE
AKHCDAFMVVGSSLVVYPAAELPYIAKKAGAKMIIVNAEPTMADPIFDVKIIGKAGEVLP
KIVEEVKRLRSEK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	9
NAD	Nicotinamide-adenine-dinucleotide	C21 H27 N7 O14 P2	4
NCA	Nicotinamide	C6 H6 N2 O	5
2PE	Nonaethylene glycol	C18 H38 O10	2
APR	Adenosine-5-diphosphoribose	C15 H23 N5 O14 P2	1

Water and common crystallization additives (SO4, EDO, PG4, PGE) are not listed.

Primary citation

Mechanism of Sirtuin Inhibition by Nicotinamide: Altering the NAD(+) Cosubstrate Specificity of a Sir2 Enzyme. Avalos, J.L., Bever, K.M., Wolberger, C. Mol Cell (2005) 17:855-868. DOI 10.1016/j.molcel.2005.02.022 · PubMed

Other PDB entries of the same protein (UniProt O30124 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4TWJ 1.65 Å, The structure of Sir2Af2 bound to a myristoylated histone peptide
1MA3 2.0 Å, Structure of a Sir2 enzyme bound to an acetylated p53 peptide
1S7G 2.3 Å, Structural Basis for the Mechanism and Regulation of Sir2 Enzymes

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