SAXSdb — 7x3p

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

NAD-dependent protein deacylase sirtuin-5, mitochondrial

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;5-[[(5~{S})-6-[[(1~{S})-1-(4-hydroxyphenyl)-2-oxidanylidene-2-(prop-2-ynylamino)ethyl]amino]-6-oxidanylidene-5-[[4-[3-(trifluoromethyl)-1,2-diazirin-3-yl]phenyl]carbonylamino]hexyl]amino]-5-sulfanylidene-pentanoic acid ; × 1 DI(HYDROXYETHYL)ETHER × 1 ZINC ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SIR5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–277； UniProt 34–310

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	7x3p
Deposition date deposition_date	2022-03-01
Structure title title	Crystal structure of human SIRT5 in complex with diazirine inhibitor 9
Keywords keywords	inhibitor, complex, 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.

7x3p__assembly_1__model_1

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

Download this curve (.dat)

7x3p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7x3p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.10 Å
Rg (electron density)	19.19 Å
Total Rg	20.12 Å
Atom count	2096
Residues	267
Excluded volume	37094 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7x3p__assembly_1__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)

Entity 1 Entity 1 polymer

Description description	NAD-dependent protein deacylase sirtuin-5, mitochondrial
Molecular weight formula_weight	30183.3 kDa
EC 编号 ec_number	2.3.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2543

ARPSSSMADFRKFFAKAKHIVIISGAGVSAESGVPTFRGAGGYWRKWQAQDLATPLAFAHNPSRVWEFYHYRREVMGSKEPNAGHRAIAECETRLGKQGRRVVVITQNIDELHRKAGTKNLLEIHGSLFKTRCTSCGVVAENYKSPICPALSGKGAPEPGTQDASIPVEKLPRCEEAGCGGLLRPHVVWFGENLDPAILEEVDRELAHCDLCLVVGTSSVVYPAAMFAPQVAARGVPVAEFNTETTPATNRFRFHFQGPCGTTLPEALACHENETVS

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	;5-[[(5~{S})-6-[[(1~{S})-1-(4-hydroxyphenyl)-2-oxidanylidene-2-(prop-2-ynylamino)ethyl]amino]-6-oxidanylidene-5-[[4-[3-(trifluoromethyl)-1,2-diazirin-3-yl]phenyl]carbonylamino]hexyl]amino]-5-sulfanylidene-pentanoic acid ;
Molecular weight formula_weight	674.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	391

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Unit-cell length a length_a	41.332 Å
Unit-cell length b length_b	65.034 Å
Unit-cell length c length_c	55.658 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.58 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.560 Å
Low-resolution limit resolution_low	27.775 Å
R factor r_factor	0.1395
R_work r_work	0.1388
R_free r_free	0.1634

Crystal structure of human SIRT5 in complex with diazirine inhibitor 9

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

NAD-dependent protein deacylase sirtuin-5, 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

7x3p__assembly_1__model_1

7x3p__assembly_1__model_1 | I(q)

7x3p__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 (5)

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 water

7. Citations (1)

Crystal structure of human SIRT5 in complex with diazirine inhibitor 9

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

NAD-dependent protein deacylase sirtuin-5, 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

7x3p__assembly_1__model_1

7x3p__assembly_1__model_1 | I(q)

7x3p__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 (5)

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 water

7. Citations (1)