SAXSdb — 3wye

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

;Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming] ;

Klebsiella pneumoniae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 4	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BUDC_KLEPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–83； UniProt 1–83 Author chain A； PDBConstruct 119–134； UniProt 119–134 Author chain A； PDBConstruct 162–181； UniProt 162–181 Author chain A； PDBConstruct 234–256； UniProt 234–256 Author chain B； PDBConstruct 1–83； UniProt 1–83 Author chain B； PDBConstruct 119–134； UniProt 119–134 Author chain B； PDBConstruct 162–181； UniProt 162–181 Author chain B； PDBConstruct 234–256； UniProt 234–256

;Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming] ;

Klebsiella pneumoniae

UniProt Q9ZNN8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 4	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BUDC_CORGT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 84–118； UniProt 86–120 Author chain A； PDBConstruct 135–161； UniProt 137–163 Author chain A； PDBConstruct 182–233； UniProt 184–235 Author chain B； PDBConstruct 84–118； UniProt 86–120 Author chain B； PDBConstruct 135–161； UniProt 137–163 Author chain B； PDBConstruct 182–233； UniProt 184–235

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	3wye
Deposition date deposition_date	2014-08-26
Structure title title	Crystal Structure of chimeric engineered (2S,3S)-butanediol dehydrogenase complexed with NAD+
Keywords keywords	;butanediol dehydrogenase, domain chimera, NAD+ complex, short-chain dehydrogenase/reductase family, Rossmann Fold, Oxidoreductase, NAD+ Binding, Oxidation/reduction ;; 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.

3wye__assembly_1__model_1

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

Download this curve (.dat)

3wye__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3wye__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.99 Å
Rg (electron density)	27.81 Å
Total Rg	28.60 Å
Atom count	7414
Residues	988
Excluded volume	132330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3wye__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 (3)

Entity 1 Entity 1 polymer

Description description	;Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming] ;
Molecular weight formula_weight	26720.4 kDa
EC 编号 ec_number	1.1.1.304,1.1.1.76,1.1.1.304,1.1.1.304,1.1.1.76,1.1.1.304,1.1.1.304,1.1.1.76,1.1.1.304,1.1.1.304
Mutation mutation	R52H, M54V,R52H, M54V,R52H, M54V,R52H, M54V,R52H, M54V,R52H, M54V,R52H, M54V
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	3871

MKKVALVTGAGQGIGKAIALRLVKDGFAVAIADYNDATAKAVASEINQAGGHAVAVKVDVSDRDQVFAAVEQARKTLGGFDVIVNNAGIAQIKPLLEVTEEDLKQIYSVNVFSVFFGIQAAVEAFKKEGHGGKIINAASIAAIQGFPILSAYSTTKFAVRGLTQTAARDLAPLGITVNGYCPGIVGTGMWEQIDAELSKINGKPIGENFKEYSSSIALGRPSVPEDVAGLVSFLASPDSDYMTGQSLLIDGGMVFN

Source Source

Source organism organism	Klebsiella pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	573
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	140

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3wyea_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

Domain ID domain_id	d3wyeb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.2 — Tyrosine-dependent oxidoreductases

CATH v4.4 (2 domains)

Domain ID domain_id	3wyeA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3wyeB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

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Unit-cell length a length_a	81.244 Å
Unit-cell length b length_b	134.617 Å
Unit-cell length c length_c	87.794 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.580 Å
Low-resolution limit resolution_low	39.279 Å
R factor r_factor	0.1829
R_work r_work	0.1820
R_free r_free	0.1988

Crystal Structure of chimeric engineered (2S,3S)-butanediol dehydrogenase complexed with NAD+

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

;Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming] ;

State in the Current Structure

Other States of the Same Protein in the Database

;Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming] ;

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

3wye__assembly_1__model_1

3wye__assembly_1__model_1 | I(q)

3wye__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of chimeric engineered (2S,3S)-butanediol dehydrogenase complexed with NAD+

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

;Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming] ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

;Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming],L-2,3-butanediol dehydrogenase,Diacetyl reductase [(S)-acetoin forming] ;

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

3wye__assembly_1__model_1

3wye__assembly_1__model_1 | I(q)

3wye__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)