SAXSdb — 6iso

▼

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

NAD-dependent protein deacetylase sirtuin-3, mitochondrial

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	ARG-THR-LYS-GLN-THR-ALA-ARG × 1 ZINC ION × 1 (2E)-BUT-2-ENAL × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	ARG-THR-LYS-GLN-THR-ALA-ARG × 1 ZINC ION × 1 (2E)-BUT-2-ENAL × 1 GLYCEROL × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	ARG-THR-LYS-GLN-THR-ALA-ARG × 1 ZINC ION × 1 (2E)-BUT-2-ENAL × 1 GLYCEROL × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	ARG-THR-LYS-GLN-THR-ALA-ARG × 1 ZINC ION × 1 (2E)-BUT-2-ENAL × 1 GLYCEROL × 1 water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	ARG-THR-LYS-GLN-THR-ALA-ARG × 1 (2E)-BUT-2-ENAL × 1 GLYCEROL × 1 water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	ARG-THR-LYS-GLN-THR-ALA-ARG × 1 ZINC ION × 1 (2E)-BUT-2-ENAL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SIR3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–274； UniProt 121–394 Author chain B； PDBConstruct 1–274； UniProt 121–394 Author chain E； PDBConstruct 1–274； UniProt 121–394 Author chain G； PDBConstruct 1–274； UniProt 121–394 Author chain I； PDBConstruct 1–274； UniProt 121–394 Author chain K； PDBConstruct 1–274； UniProt 121–394

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6iso
Deposition date deposition_date	2018-11-17
Structure title title	Human SIRT3 Recognizing H3K4cr
Keywords keywords	Posttranslational modification, Sirtuins, Histones, Complex., HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6iso__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6iso__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6iso__assembly_5__model_1 | P(r) · Pending

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

Rg（Guinier）	17.86 Å
Rg (electron density)	16.44 Å
Total Rg	17.58 Å
Atom count	1553
Residues	200
Excluded volume	27964 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6iso__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6iso__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6iso__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6iso__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`6iso__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`6iso__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Molecular weight formula_weight	30566.3 kDa
EC 编号 ec_number	3.5.1.-
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E,G,I,K
Atom count atom_count	12241

GKLSLQDVAELIRARACQRVVVMVGAGISTPSGIPDFRSPGSGLYSNLQQYDLPYPEAIFELPFFFHNPKPFFTLAKELYPGNYKPNVTHYFLRLLHDKGLLLRLYTQNIDGLERVSGIPASKLVEAHGTFASATCTVCQRPFPGEDIRADVMADRVPRCPVCTGVVKPDIVFFGEPLPQRFLLHVVDFPMADLLLILGTSLEVEPFASLTEAVRSSVPRLLINRDLVGPLAWHPRSRDVAQLGDVVHGVESLVELLGWTEEMRDLVQRETGKLA

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-Pichia pastoris shuttle vector pPpARG4

Entity 2 Entity 2 polymer

Description description	ARG-THR-LYS-GLN-THR-ALA-ARG
Molecular weight formula_weight	863.0 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,F,H,L,J

RTKQTAR

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	(2E)-BUT-2-ENAL
Molecular weight formula_weight	70.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	181

▼

6. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

Domain ID domain_id	6isoA01
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	6isoA02
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	6isoB01
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	6isoB02
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	6isoE01
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	6isoE02
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	6isoG01
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	6isoG02
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	6isoI01
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	6isoI02
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	6isoK00
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

▶

Unit-cell length a length_a	138.085 Å
Unit-cell length b length_b	138.085 Å
Unit-cell length c length_c	225.342 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	48

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.950 Å
Low-resolution limit resolution_low	39.250 Å
R factor r_factor	0.2241
R_work r_work	0.2214
R_free r_free	0.2752

Human SIRT3 Recognizing H3K4cr

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

NAD-dependent protein deacetylase sirtuin-3, mitochondrial

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

6iso__assembly_5__model_1

6iso__assembly_5__model_1 | I(q)

6iso__assembly_5__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

7. Citations (1)

Human SIRT3 Recognizing H3K4cr

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

NAD-dependent protein deacetylase sirtuin-3, mitochondrial

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

6iso__assembly_5__model_1

6iso__assembly_5__model_1 | I(q)

6iso__assembly_5__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

7. Citations (1)