6nr0

SIRT2(56-356) with covalent intermediate between mechanism-based inhibitor Glucose-TM-1beta and 1'-SH ADP-ribose

Method: X-RAY DIFFRACTION

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

NAD-dependent protein deacetylase sirtuin-2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 N~2~-[3-(2-hydroxyethoxy)propanoyl]-N-phenyl-N~6~-tetradecanethioyl-L-lysinamide × 2 ;[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-sulfanyl-oxolan-2-yl]methyl hydrogen phosphate ; × 2 SODIUM ION × 4 SULFATE ION × 2 GLYCEROL × 4 water × 2	Review required
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 N~2~-[3-(2-hydroxyethoxy)propanoyl]-N-phenyl-N~6~-tetradecanethioyl-L-lysinamide × 1 ;[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-sulfanyl-oxolan-2-yl]methyl hydrogen phosphate ; × 1 SODIUM ION × 2 SULFATE ION × 1 GLYCEROL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SIR2_HUMAN
Isoform	Q8IXJ6-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–319； UniProt 1–319 Author chain B； PDBConstruct 1–319； UniProt 1–319

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	6nr0
Deposition date deposition_date	2019-01-22
Structure title title	SIRT2(56-356) with covalent intermediate between mechanism-based inhibitor Glucose-TM-1beta and 1'-SH ADP-ribose
Keywords keywords	inhibitor, intermediate, deacylase, HYDROLASE, hydrolase-hydrolase inhibitor complex; hydrolase/hydrolase inhibitor
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.

6nr0__assembly_1__model_1

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

Download this curve (.dat)

6nr0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6nr0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.99 Å
Rg (electron density)	26.94 Å
Total Rg	27.74 Å
Atom count	9301
Residues	580
Excluded volume	86106 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6nr0__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6nr0__assembly_2__model_1`	monomeric （1）	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 (8)

Entity 1 Entity 1 polymer

Description description	NAD-dependent protein deacetylase sirtuin-2
Molecular weight formula_weight	36159.7 kDa
EC 编号 ec_number	3.5.1.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9501

MDFLRNLFSQTLSLGSQKERLLDELTLEGVARYMQSERCRRVICLVGAGISTSAGIPDFRSPSTGLYDNLEKYHLPYPEAIFEISYFKKHPEPFFALAKELYPGQFKPTICHYFMRLLKDKGLLLRCYTQNIDTLERIAGLEQEDLVEAHGTFYTSHCVSASCRHEYPLSWMKEKIFSEVTPKCEDCQSLVKPDIVFFGESLPARFFSCMQSDFLKVDLLLVMGTSLQVQPFASLISKAPLSTPRLLINKEKAGQSDPFLGMIMGLGGGMDFDSKKAYRDVAWLGECDQGCLALAELLGWKKELEDLVRREHASIDAQS

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

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	2

Entity 3 Entity 3 non-polymer

Description description	N~2~-[3-(2-hydroxyethoxy)propanoyl]-N-phenyl-N~6~-tetradecanethioyl-L-lysinamide
Molecular weight formula_weight	563.8 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	;[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-sulfanyl-oxolan-2-yl]methyl hydrogen phosphate ;
Molecular weight formula_weight	575.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	nat
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	134

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6nr0a_
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	d6nr0b_
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 (4 domains)

Domain ID domain_id	6nr0A01
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	6nr0A02
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	6nr0B01
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	6nr0B02
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	82.310 Å
Unit-cell length b length_b	76.840 Å
Unit-cell length c length_c	114.461 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.87 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	63.690 Å
R factor r_factor	0.2230
R_work r_work	0.2202
R_free r_free	0.2562

SIRT2(56-356) with covalent intermediate between mechanism-based inhibitor Glucose-TM-1beta and 1'-SH ADP-ribose

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

NAD-dependent protein deacetylase sirtuin-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

6nr0__assembly_1__model_1

6nr0__assembly_1__model_1 | I(q)

6nr0__assembly_1__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 (8)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

SIRT2(56-356) with covalent intermediate between mechanism-based inhibitor Glucose-TM-1beta and 1'-SH ADP-ribose

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

NAD-dependent protein deacetylase sirtuin-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

6nr0__assembly_1__model_1

6nr0__assembly_1__model_1 | I(q)

6nr0__assembly_1__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 (8)

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 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)