1s20

A novel NAD binding protein revealed by the crystal structure of E. Coli 2,3-diketogulonate reductase (YiaK) NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER82

Method: X-RAY DIFFRACTION

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

Hypothetical oxidoreductase yiaK

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	L(+)-TARTARIC ACID × 2 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	L(+)-TARTARIC ACID × 1 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	L(+)-TARTARIC ACID × 1 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	L(+)-TARTARIC ACID × 2 NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YIAK_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–332； UniProt 1–332 Author chain B； PDBConstruct 1–332； UniProt 1–332 Author chain C； PDBConstruct 1–332； UniProt 1–332 Author chain D； PDBConstruct 1–332； UniProt 1–332 Author chain E； PDBConstruct 1–332； UniProt 1–332 Author chain F； PDBConstruct 1–332； UniProt 1–332 Author chain G； PDBConstruct 1–332； UniProt 1–332 Author chain H； PDBConstruct 1–332； UniProt 1–332

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	1s20
Deposition date deposition_date	2004-01-07
Structure title title	A novel NAD binding protein revealed by the crystal structure of E. Coli 2,3-diketogulonate reductase (YiaK) NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER82
Keywords keywords	;alpha beta dimeric protein, OXIDOREDUCTASE, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG ;; OXIDOREDUCTASE
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.

1s20__assembly_1__model_1

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

Download this curve (.dat)

1s20__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1s20__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.69 Å
Rg (electron density)	24.80 Å
Total Rg	25.26 Å
Atom count	5266
Residues	638
Excluded volume	93522 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1s20__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1s20__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1s20__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1s20__assembly_4__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 (4)

Entity 1 Entity 1 polymer

Description description	Hypothetical oxidoreductase yiaK
Molecular weight formula_weight	38385.2 kDa
EC 编号 ec_number	1.1.1.-
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	22358

MKVTFEQLKAAFNRVLISRGVDSETADACAEMFARTTESGVYSHGVNRFPRFIQQLENGDIIPDAQPKRITSLGAIEQWDAQRSIGNLTAKKMMDRAIELAADHGIGLVALRNANHWMRGGSYGWQAAEKGYIGICWTNSIAVMPPWGAKECRIGTNPLIVAIPSTPITMVDMSMSMFSYGMLEVNRLAGRQLPVDGGFDDEGNLTKEPGVIEKNRRILPMGYWKGSGMSIVLDMIATLLSDGASVAEVTQDNSDEYGISQIFIAIEVDKLIDGPTRDAKLQRIMDYVTSAERADENQAIRLPGHEFTTLLAENRRNGITVDDSVWAKIQALLEHHHHHH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	L(+)-TARTARIC ACID
Molecular weight formula_weight	150.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1401

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6. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d1s20a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.122 — L-sulfolactate dehydrogenase-like
Superfamily Superfamily superfamily	c.122.1 — L-sulfolactate dehydrogenase-like
Family Family family	c.122.1.1 — L-sulfolactate dehydrogenase-like

Domain ID domain_id	d1s20a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1s20b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.122 — L-sulfolactate dehydrogenase-like
Superfamily Superfamily superfamily	c.122.1 — L-sulfolactate dehydrogenase-like
Family Family family	c.122.1.1 — L-sulfolactate dehydrogenase-like

Domain ID domain_id	d1s20b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1s20c1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.122 — L-sulfolactate dehydrogenase-like
Superfamily Superfamily superfamily	c.122.1 — L-sulfolactate dehydrogenase-like
Family Family family	c.122.1.1 — L-sulfolactate dehydrogenase-like

Domain ID domain_id	d1s20c2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1s20d1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.122 — L-sulfolactate dehydrogenase-like
Superfamily Superfamily superfamily	c.122.1 — L-sulfolactate dehydrogenase-like
Family Family family	c.122.1.1 — L-sulfolactate dehydrogenase-like

Domain ID domain_id	d1s20d2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1s20e1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.122 — L-sulfolactate dehydrogenase-like
Superfamily Superfamily superfamily	c.122.1 — L-sulfolactate dehydrogenase-like
Family Family family	c.122.1.1 — L-sulfolactate dehydrogenase-like

Domain ID domain_id	d1s20e2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1s20f1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.122 — L-sulfolactate dehydrogenase-like
Superfamily Superfamily superfamily	c.122.1 — L-sulfolactate dehydrogenase-like
Family Family family	c.122.1.1 — L-sulfolactate dehydrogenase-like

Domain ID domain_id	d1s20f2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1s20g1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.122 — L-sulfolactate dehydrogenase-like
Superfamily Superfamily superfamily	c.122.1 — L-sulfolactate dehydrogenase-like
Family Family family	c.122.1.1 — L-sulfolactate dehydrogenase-like

Domain ID domain_id	d1s20g2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1s20h1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.122 — L-sulfolactate dehydrogenase-like
Superfamily Superfamily superfamily	c.122.1 — L-sulfolactate dehydrogenase-like
Family Family family	c.122.1.1 — L-sulfolactate dehydrogenase-like

Domain ID domain_id	d1s20h2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (24 domains)

Domain ID domain_id	1s20A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel

Domain ID domain_id	1s20A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain

Domain ID domain_id	1s20A03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	50 — Hypothetical oxidoreductase yiak; domain 3

Domain ID domain_id	1s20B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel

Domain ID domain_id	1s20B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain

Domain ID domain_id	1s20B03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	50 — Hypothetical oxidoreductase yiak; domain 3

Domain ID domain_id	1s20C01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel

Domain ID domain_id	1s20C02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain

Domain ID domain_id	1s20C03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	50 — Hypothetical oxidoreductase yiak; domain 3

Domain ID domain_id	1s20D01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel

Domain ID domain_id	1s20D02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain

Domain ID domain_id	1s20D03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	50 — Hypothetical oxidoreductase yiak; domain 3

Domain ID domain_id	1s20E01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel

Domain ID domain_id	1s20E02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain

Domain ID domain_id	1s20E03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	50 — Hypothetical oxidoreductase yiak; domain 3

Domain ID domain_id	1s20F01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel

Domain ID domain_id	1s20F02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain

Domain ID domain_id	1s20F03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	50 — Hypothetical oxidoreductase yiak; domain 3

Domain ID domain_id	1s20G01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel

Domain ID domain_id	1s20G02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain

Domain ID domain_id	1s20G03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	50 — Hypothetical oxidoreductase yiak; domain 3

Domain ID domain_id	1s20H01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1530 — Hypothetical Oxidoreductase Yiak; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel

Domain ID domain_id	1s20H02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1370 — Ribosomal Protein S8; Chain: A, domain 1
Homologous superfamily homologous superfamily	60 — Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain

Domain ID domain_id	1s20H03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	50 — Hypothetical oxidoreductase yiak; domain 3

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Unit-cell length a length_a	75.524 Å
Unit-cell length b length_b	81.275 Å
Unit-cell length c length_c	113.215 Å
Unit-cell angle α angle_alpha	79.55 °
Unit-cell angle β angle_beta	77.22 °
Unit-cell angle γ angle_gamma	82.01 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	24.020 Å
R factor r_factor	0.1900
R_work r_work	0.1910
R_free r_free	0.2500

A novel NAD binding protein revealed by the crystal structure of E. Coli 2,3-diketogulonate reductase (YiaK) NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER82

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

Hypothetical oxidoreductase yiaK

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

1s20__assembly_1__model_1

1s20__assembly_1__model_1 | I(q)

1s20__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) 40 domains

SCOP 2.08 (16 domains)

CATH v4.4 (24 domains)

7. Citations (1)

A novel NAD binding protein revealed by the crystal structure of E. Coli 2,3-diketogulonate reductase (YiaK) NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER82

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

Hypothetical oxidoreductase yiaK

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

1s20__assembly_1__model_1

1s20__assembly_1__model_1 | I(q)

1s20__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) 40 domains

SCOP 2.08 (16 domains)

CATH v4.4 (24 domains)

7. Citations (1)