1yc2

Sir2Af2-NAD-ADPribose-nicotinamide

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

NAD-dependent deacetylase 2

Archaeoglobus fulgidus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 2 SULFATE ION × 2 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 NICOTINAMIDE × 1 1,2-ETHANEDIOL × 3 water × 1	Consistent with protein count
10	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 SULFATE ION × 4 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 NICOTINAMIDE × 1 NONAETHYLENE GLYCOL × 1 TETRAETHYLENE GLYCOL × 1 TRIETHYLENE GLYCOL × 1 water × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 2 SULFATE ION × 4 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 NICOTINAMIDE × 1 1,2-ETHANEDIOL × 2 NONAETHYLENE GLYCOL × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 2 SULFATE ION × 3 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 NONAETHYLENE GLYCOL × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ZINC ION × 2 SULFATE ION × 1 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 NICOTINAMIDE × 1 TETRAETHYLENE GLYCOL × 1 TRIETHYLENE GLYCOL × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	ZINC ION × 1 NICOTINAMIDE × 2 ADENOSINE-5-DIPHOSPHORIBOSE × 1 water × 1	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 8 SULFATE ION × 10 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 NICOTINAMIDE × 3 1,2-ETHANEDIOL × 5 NONAETHYLENE GLYCOL × 2 TETRAETHYLENE GLYCOL × 1 TRIETHYLENE GLYCOL × 1 water × 4	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 SULFATE ION × 5 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 NICOTINAMIDE × 1 1,2-ETHANEDIOL × 3 NONAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count
8	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 SULFATE ION × 5 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 NICOTINAMIDE × 2 1,2-ETHANEDIOL × 2 NONAETHYLENE GLYCOL × 1 TETRAETHYLENE GLYCOL × 1 TRIETHYLENE GLYCOL × 1 water × 2	Consistent with protein count
9	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 SULFATE ION × 6 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 NICOTINAMIDE × 2 1,2-ETHANEDIOL × 5 NONAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NPD2_ARCFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–253； UniProt 1–253 Author chain B； PDBConstruct 1–253； UniProt 1–253 Author chain C； PDBConstruct 1–253； UniProt 1–253 Author chain D； PDBConstruct 1–253； UniProt 1–253 Author chain E； PDBConstruct 1–253； UniProt 1–253

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1yc2
Deposition date deposition_date	2004-12-21
Structure title title	Sir2Af2-NAD-ADPribose-nicotinamide
Keywords keywords	sir2, sirtuin, nicotinamide, NAD, ADPribose, ternary complex, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1yc2__assembly_8__model_1

Assembly 8 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1yc2__assembly_8__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yc2__assembly_8__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	26.32 Å
Rg (electron density)	25.57 Å
Total Rg	26.37 Å
Atom count	4130
Residues	503
Excluded volume	73652 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yc2__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1yc2__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1yc2__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1yc2__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1yc2__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1yc2__assembly_6__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`1yc2__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`1yc2__assembly_8__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`1yc2__assembly_9__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`1yc2__assembly_10__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	NAD-dependent deacetylase 2
Molecular weight formula_weight	28537.0 kDa
EC 编号 ec_number	3.5.1.-
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	10409

MEDEIRKAAEILAKSKHAVVFTGAGISAESGIPTFRGEDGLWRKYDPEEVASISGFKRNPRAFWEFSMEMKDKLFAEPNPAHYAIAELERMGIVKAVITQNIDMLHQRAGSRRVLELHGSMDKLDCLDCHETYDWSEFVEDFNKGEIPRCRKCGSYYVKPRVVLFGEPLPQRTLFEAIEEAKHCDAFMVVGSSLVVYPAAELPYIAKKAGAKMIIVNAEPTMADPIFDVKIIGKAGEVLPKIVEEVKRLRSEK

Source Source

Source organism organism	Archaeoglobus fulgidus
NCBI taxonomy ID ncbi_taxonomy_id	2234
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	NICOTINAMIDE
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 non-polymer

Description description	NONAETHYLENE GLYCOL
Molecular weight formula_weight	414.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	ADENOSINE-5-DIPHOSPHORIBOSE
Molecular weight formula_weight	559.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	249

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1yc2a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
Family Family family	c.31.1.5 — Sir2 family of transcriptional regulators

Domain ID domain_id	d1yc2b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
Family Family family	c.31.1.5 — Sir2 family of transcriptional regulators

Domain ID domain_id	d1yc2c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
Family Family family	c.31.1.5 — Sir2 family of transcriptional regulators

Domain ID domain_id	d1yc2d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
Family Family family	c.31.1.5 — Sir2 family of transcriptional regulators

Domain ID domain_id	d1yc2e_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
Family Family family	c.31.1.5 — Sir2 family of transcriptional regulators

CATH v4.4 (10 domains)

Domain ID domain_id	1yc2A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	1yc2A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

Domain ID domain_id	1yc2B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	1yc2B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

Domain ID domain_id	1yc2C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	1yc2C02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

Domain ID domain_id	1yc2D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	1yc2D02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

Domain ID domain_id	1yc2E01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	1yc2E02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

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Unit-cell length a length_a	105.122 Å
Unit-cell length b length_b	181.562 Å
Unit-cell length c length_c	79.025 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2118
R_work r_work	0.2093
R_free r_free	0.2551

Sir2Af2-NAD-ADPribose-nicotinamide

1. Protein Identity and Related Structures Protein Identity & Related Structures

NAD-dependent deacetylase 2

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1yc2__assembly_8__model_1

1yc2__assembly_8__model_1 | I(q)

1yc2__assembly_8__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (5 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Sir2Af2-NAD-ADPribose-nicotinamide

1. Protein Identity and Related Structures Protein Identity & Related Structures

NAD-dependent deacetylase 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1yc2__assembly_8__model_1

1yc2__assembly_8__model_1 | I(q)

1yc2__assembly_8__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (5 domains)

CATH v4.4 (10 domains)

7. Citations (1)