SAXSdb — 1yt5

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

inorganic polyphosphate/ATP-NAD kinase

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 13 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 5 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 18 water × 4	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 18 water × 4	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 9 water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 9 water × 2	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 9 water × 2	Consistent with protein count
8	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 9 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPNK_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–258； UniProt 1–258 Author chain B； PDBConstruct 1–258； UniProt 1–258 Author chain C； PDBConstruct 1–258； UniProt 1–258 Author chain D； PDBConstruct 1–258； UniProt 1–258

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	1yt5
Deposition date deposition_date	2005-02-09
Structure title title	Crystal structure of NAD kinase from Thermotoga maritima
Keywords keywords	;domain 1: alpha/beta domain2: beta sandwich, Structural Genomics, PSI, Protein Structure Initiative, Berkeley Structural Genomics Center, BSGC, Transferase ;; TRANSFERASE
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.

1yt5__assembly_6__model_1

Assembly 6 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1yt5__assembly_6__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yt5__assembly_6__model_1 | P(r) · Pending

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

Rg（Guinier）	26.88 Å
Rg (electron density)	25.98 Å
Total Rg	26.78 Å
Atom count	4104
Residues	508
Excluded volume	73252 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yt5__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1yt5__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1yt5__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1yt5__assembly_4__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1yt5__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1yt5__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`1yt5__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`1yt5__assembly_8__model_1`	dimeric （2）	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 (3)

Entity 1 Entity 1 polymer

Description description	inorganic polyphosphate/ATP-NAD kinase
Molecular weight formula_weight	29280.6 kDa
EC 编号 ec_number	2.7.1.23
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8357

MKIAILYREEREKEGEFLKEKISKEHEVIEFGEANAPGRVTADLIVVVGGDGTVLKAAKKAADGTPMVGFKAGRLGFLTSYTLDEIDRFLEDLRNWNFREETRWFIQIESELGNHLALNDVTLERDLSGKMVEIEVEVEHHSSMWFFADGVVISTPTGSTAYSLSIGGPIIFPECEVLEISPIAPQFFLTRSVVIPSNFKVVVESQRDINMLVDGVLTGKTKRIEVKKSRRYVRILRPPEYDYVTVIRDKLGYGRRIE

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli K12

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	18

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	120

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	1yt5A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10330 — Probable inorganic polyphosphate/atp-NAD kinase; domain 1

Domain ID domain_id	1yt5A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily	30 — Probable inorganic polyphosphate/atp-NAD kinase; domain 2

Domain ID domain_id	1yt5B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10330 — Probable inorganic polyphosphate/atp-NAD kinase; domain 1

Domain ID domain_id	1yt5B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily	30 — Probable inorganic polyphosphate/atp-NAD kinase; domain 2

Domain ID domain_id	1yt5C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10330 — Probable inorganic polyphosphate/atp-NAD kinase; domain 1

Domain ID domain_id	1yt5C02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily	30 — Probable inorganic polyphosphate/atp-NAD kinase; domain 2

Domain ID domain_id	1yt5D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10330 — Probable inorganic polyphosphate/atp-NAD kinase; domain 1

Domain ID domain_id	1yt5D02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily	30 — Probable inorganic polyphosphate/atp-NAD kinase; domain 2

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Unit-cell length a length_a	131.448 Å
Unit-cell length b length_b	137.153 Å
Unit-cell length c length_c	58.253 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	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	0.2170
R_work r_work	0.2130
R_free r_free	0.2800

Crystal structure of NAD kinase from Thermotoga maritima

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

inorganic polyphosphate/ATP-NAD kinase

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

1yt5__assembly_6__model_1

1yt5__assembly_6__model_1 | I(q)

1yt5__assembly_6__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of NAD kinase from Thermotoga maritima

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

inorganic polyphosphate/ATP-NAD kinase

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

1yt5__assembly_6__model_1

1yt5__assembly_6__model_1 | I(q)

1yt5__assembly_6__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)