SAXSdb — 3afo

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

NADH kinase POS5

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 4 (4S)-2-METHYL-2,4-PENTANEDIOL × 8 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POS5_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–388； UniProt 27–414 Author chain B； PDBConstruct 1–388； UniProt 27–414

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	3afo
Deposition date deposition_date	2010-03-10
Structure title title	Crystal Structure of Yeast NADH Kinase complexed with NADH
Keywords keywords	Alpha/beta+beta sandwich, ATP-binding, Kinase, Mitochondrion, NAD, NADP, Nucleotide-binding, Transferase, Transit peptide; 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.

3afo__assembly_1__model_1

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

Download this curve (.dat)

3afo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3afo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.80 Å
Rg (electron density)	36.07 Å
Total Rg	36.36 Å
Atom count	11164
Residues	1402
Excluded volume	199500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3afo__assembly_1__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	NADH kinase POS5
Molecular weight formula_weight	43073.9 kDa
EC 编号 ec_number	2.7.1.86
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6305

LQSGSKFVKIKPVNNLRSSSSADFVSPPNSKLQSLIWQNPLQNVYITKKPWTPSTREAMVEFITHLHESYPEVNVIVQPDVAEEISQDFKSPLENDPNRPHILYTGPEQDIVNRTDLLVTLGGDGTILHGVSMFGNTQVPPVLAFALGTLGFLSPFDFKEHKKVFQEVISSRAKCLHRTRLECHLKKKDSNSSIVTHAMNDIFLHRGNSPHLTNLDIFIDGEFLTRTTADGVALATPTGSTAYSLSAGGSIVSPLVPAILMTPICPRSLSFRPLILPHSSHIRIKIGSKLNQKPVNSVVKLSVDGIPQQDLDVGDEIYVINEVGTIYIDGTQLPTTRKTENDFNNSKKPKRSGIYCVAKTENDWIRGINELLGFNSSFRLTKRQTDND

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Molecular weight formula_weight	665.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	478

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3afoA01
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	3afoA02
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	3afoB01
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	3afoB02
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	98.685 Å
Unit-cell length b length_b	132.782 Å
Unit-cell length c length_c	59.636 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	8

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1997
R_work r_work	0.1974
R_free r_free	0.2438

Crystal Structure of Yeast NADH Kinase complexed with NADH

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

NADH kinase POS5

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

3afo__assembly_1__model_1

3afo__assembly_1__model_1 | I(q)

3afo__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Yeast NADH Kinase complexed with NADH

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

NADH kinase POS5

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

3afo__assembly_1__model_1

3afo__assembly_1__model_1 | I(q)

3afo__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)