SAXSdb — 9v12

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

Xanthosine/inosine triphosphate pyrophosphatase

Archangium gephyra

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	NAD-dependent protein deacetylase × 8 （A0AAC8TGL7） ;2'-deoxyinosine 5'-triphosphate ; × 8 ZINC ION × 8 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0AAC8QDB0_9BACT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain I； PDBConstruct 1–181； UniProt 1–181 Author chain K； PDBConstruct 1–181； UniProt 1–181 Author chain M； PDBConstruct 1–181； UniProt 1–181 Author chain O； PDBConstruct 1–181； UniProt 1–181 Author chain R； PDBConstruct 1–181； UniProt 1–181 Author chain T； PDBConstruct 1–181； UniProt 1–181 Author chain V； PDBConstruct 1–181； UniProt 1–181 Author chain X； PDBConstruct 1–181； UniProt 1–181

NAD-dependent protein deacetylase

Archangium gephyra

UniProt A0AAC8TGL7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 16	Xanthosine/inosine triphosphate pyrophosphatase × 8 （A0AAC8QDB0） ;2'-deoxyinosine 5'-triphosphate ; × 8 ZINC ION × 8 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0AAC8TGL7_9BACT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain i； PDBConstruct 1–278； UniProt 1–278 Author chain j； PDBConstruct 1–278； UniProt 1–278 Author chain k； PDBConstruct 1–278； UniProt 1–278 Author chain l； PDBConstruct 1–278； UniProt 1–278 Author chain m； PDBConstruct 1–278； UniProt 1–278 Author chain n； PDBConstruct 1–278； UniProt 1–278 Author chain o； PDBConstruct 1–278； UniProt 1–278 Author chain p； PDBConstruct 1–278； UniProt 1–278

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	9v12
Deposition date deposition_date	2025-05-19
Structure title title	Helical structure of KomBCMUT in complex with dITP and NAD
Keywords keywords	Cryo-EM, Sir2, CELL INVASION; CELL INVASION
Experimental Method method	ELECTRON MICROSCOPY

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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.

9v12__assembly_1__model_1

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

Download this curve (.dat)

9v12__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9v12__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	52.62 Å
Rg (electron density)	52.05 Å
Total Rg	52.33 Å
Atom count	29320
Residues	3656
Excluded volume	520350 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9v12__assembly_1__model_1`	hexadecameric （16）	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	Xanthosine/inosine triphosphate pyrophosphatase
Molecular weight formula_weight	20012.0 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,K,M,O,R,T,V,X
Atom count atom_count	29320

MAPTWFYNTTNSEKLRELQHVLGGSAKLGYLTAKVTEILDVDLETVIRAKAIAAYRAVRVPVIVEHGALCIDALNGLPGALVKPFWESLDTRLCEVIPAGQRTARARGALCYCDGRERHVLIEETEGEIAPSARGTGGFHWDPIFIPKGQTRTFAEMSLDEKLSFSPLGRLHTRLRTELGL

Source Source

Source organism organism	Archangium gephyra
NCBI taxonomy ID ncbi_taxonomy_id	48
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	NAD-dependent protein deacetylase
Molecular weight formula_weight	31260.6 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	i,j,k,l,m,n,o,p

MTTLTLSEAAPLLKKEFREGRLIPFLGAGFSKPLKLPDGSQLIASLAKTLGFEPELFDMHGRFEQLAEFFAISAPNRLQRLVYEMSLSFDSAEAEALREKSPMHRALAALDWRTIYTTAYDKHVEGALRDAGKQAAVLASFADFQGPRARDVCEVIKFAGTLDQPDTIVLTESSYFQRMALDAPPDQRLRADLLANSFLFIGYSFSDTNIRYIWYRMNQLREQSQLGVKHSQARRCFFATHGAGLVQPDILQQWNIDVIQLDPTDKSASVARLLESIA

Source Source

Source organism organism	Archangium gephyra
NCBI taxonomy ID ncbi_taxonomy_id	48
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	;2'-deoxyinosine 5'-triphosphate ;
Molecular weight formula_weight	492.2 kDa
Source method src_method	syn
Copy count entity_count	8

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	8

Entity 5 Entity 5 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	8

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Resolution resolution	2.57 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	597778

Helical structure of KomBCMUT in complex with dITP and NAD

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

Xanthosine/inosine triphosphate pyrophosphatase

State in the Current Structure

Other States of the Same Protein in the Database

NAD-dependent protein deacetylase

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

9v12__assembly_1__model_1

9v12__assembly_1__model_1 | I(q)

9v12__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)

Helical structure of KomBCMUT in complex with dITP and NAD

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

Xanthosine/inosine triphosphate pyrophosphatase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NAD-dependent protein deacetylase

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

9v12__assembly_1__model_1

9v12__assembly_1__model_1 | I(q)

9v12__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)