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4bn5

Structure of human SIRT3 in complex with SRT1720 inhibitor

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL

HOMO SAPIENS

UniProt Q9NTG7

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZINC ION × 1 Consistent with protein count
10 Protein monomer Monomer Protein 1 CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZINC ION × 1 Consistent with protein count
11 Protein monomer Monomer Protein 1 CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZINC ION × 1 GLYCEROL × 1 Consistent with protein count
12 Protein monomer Monomer Protein 1 CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZINC ION × 1 GLYCEROL × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZINC ION × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZINC ION × 1 GLYCEROL × 1 Consistent with protein count
4 Protein monomer Monomer Protein 1 CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZINC ION × 1 GLYCEROL × 1 Consistent with protein count
5 Protein monomer Monomer Protein 1 CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZINC ION × 1 Consistent with protein count
6 Protein monomer Monomer Protein 1 CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZINC ION × 1 Consistent with protein count
7 Protein monomer Monomer Protein 1 CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZINC ION × 1 Consistent with protein count
8 Protein monomer Monomer Protein 1 CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZINC ION × 1 Consistent with protein count
9 Protein monomer Monomer Protein 1 CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 N-{2-[3-(piperazin-1-ylmethyl)imidazo[2,1-b][1,3]thiazol-6-yl]phenyl}quinoxaline-2-carboxamide × 1 ZINC ION × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3gls 3gls 3gls 3gls 3gls 3gls 4bn4 4bn5 4bn5 4bn5 4bn5 4bn5

38 assemblies; showing the first 12

Homodimer
9ktk 9ktk

2 assemblies

Homotetramer
9ktk

1 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
3glr 3glt 3glu 4bve 4bvf 4bvg 4c78 4c7b 4fvt 4fz3 4hd8 5bwn

50 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name SIR3_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–281； UniProt 119–399 Author chain B； PDBConstruct 1–281； UniProt 119–399 Author chain C； PDBConstruct 1–281； UniProt 119–399 Author chain D； PDBConstruct 1–281； UniProt 119–399 Author chain E； PDBConstruct 1–281； UniProt 119–399 Author chain F； PDBConstruct 1–281； UniProt 119–399 Author chain G； PDBConstruct 1–281； UniProt 119–399 Author chain H； PDBConstruct 1–281； UniProt 119–399 Author chain I； PDBConstruct 1–281； UniProt 119–399 Author chain J； PDBConstruct 1–281； UniProt 119–399 Author chain K； PDBConstruct 1–281； UniProt 119–399 Author chain L； PDBConstruct 1–281； UniProt 119–399

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_id4bn5
Deposition date deposition_date2013-05-13
Structure title titleStructure of human SIRT3 in complex with SRT1720 inhibitor
Keywords keywordsHYDROLASE, LYSINE DEACETYLASE, ADP RIBOSE; HYDROLASE
Experimental Method methodX-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.

4bn5__assembly_1__model_1

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

Download this curve (.dat)

4bn5__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4bn5__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）20.53 Å
Rg (electron density)19.42 Å
Total Rg20.43 Å
Atom count2223
Residues273
Excluded volume39786 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4bn5__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4bn5__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 4bn5__assembly_3__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 4bn5__assembly_4__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 4bn5__assembly_5__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 4bn5__assembly_6__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
7 1 4bn5__assembly_7__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
8 1 4bn5__assembly_8__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
9 1 4bn5__assembly_9__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
10 1 4bn5__assembly_10__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
11 1 4bn5__assembly_11__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
12 1 4bn5__assembly_12__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 (5)

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6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id4bn5A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id4bn5A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily10 — SIR2/SIRT2 'Small Domain'
Domain ID domain_id4bn5B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id4bn5B02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily10 — SIR2/SIRT2 'Small Domain'
Domain ID domain_id4bn5C01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id4bn5C02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily10 — SIR2/SIRT2 'Small Domain'
Domain ID domain_id4bn5D01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id4bn5D02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily10 — SIR2/SIRT2 'Small Domain'
Domain ID domain_id4bn5E01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id4bn5E02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily10 — SIR2/SIRT2 'Small Domain'
Domain ID domain_id4bn5F01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id4bn5F02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily10 — SIR2/SIRT2 'Small Domain'
Domain ID domain_id4bn5G01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id4bn5G02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily10 — SIR2/SIRT2 'Small Domain'
Domain ID domain_id4bn5H01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id4bn5H02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily10 — SIR2/SIRT2 'Small Domain'
Domain ID domain_id4bn5I01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id4bn5I02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily10 — SIR2/SIRT2 'Small Domain'
Domain ID domain_id4bn5J01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id4bn5J02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily10 — SIR2/SIRT2 'Small Domain'
Domain ID domain_id4bn5K01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id4bn5K02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily10 — SIR2/SIRT2 'Small Domain'
Domain ID domain_id4bn5L01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1220 — TPP-binding domain
Domain ID domain_id4bn5L02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily10 — SIR2/SIRT2 'Small Domain'
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7. Citations (1)