3gdn

Almond hydroxynitrile lyase in complex with benzaldehyde

Method: X-RAY DIFFRACTION

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

R-oxynitrile lyase isoenzyme 1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 2	alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 benzaldehyde × 1 (2R)-hydroxy(phenyl)ethanenitrile × 2 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 2	;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 benzaldehyde × 1 (2R)-hydroxy(phenyl)ethanenitrile × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q945K2_PRUDU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–521； UniProt 28–548 Author chain B； PDBConstruct 1–521； UniProt 28–548

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	3gdn
Deposition date deposition_date	2009-02-24
Structure title title	Almond hydroxynitrile lyase in complex with benzaldehyde
Keywords keywords	HYDROXYNITRILE LYASE, FLAVIN, GMC OXIDOREDUCTASE, ALMOND, CYANOGENESIS, Flavoprotein, Lyase; LYASE
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.

3gdn__assembly_1__model_1

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

Download this curve (.dat)

3gdn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gdn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.46 Å
Rg (electron density)	22.51 Å
Total Rg	23.44 Å
Atom count	4166
Residues	521
Excluded volume	73644 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gdn__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3gdn__assembly_2__model_1`	monomeric （1）	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 (10)

Entity 1 Entity 1 polymer

Description description	R-oxynitrile lyase isoenzyme 1
Molecular weight formula_weight	56535.8 kDa
EC 编号 ec_number	4.1.2.10
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9681

LATTSDHDFSYLSFAYDATDLELEGSYDYVIVGGGTSGCPLAATLSEKYKVLVLERGSLPTAYPNVLTADGFVYNLQQEDDGKTPVERFVSEDGIDNVRGRVLGGTSIINAGVYARANTSIYSASGVDWDMDLVNQTYEWVEDTIVYKPNSQSWQSVTKTAFLEAGVHPNHGFSLDHEEGTRITGSTFDNKGTRHAADELLNKGNSNNLRVGVHASVEKIIFSNAPGLTATGVIYRDSNGTPHQAFVRSKGEVIVSAGTIGTPQLLLLSGVGPESYLSSLNIPVVLSHPYVGQFLHDNPRNFINILPPNPIEPTIVTVLGISNDFYQCSFSSLPFTTPPFGFFPSSSYPLPNSTFAHFASKVAGPLSYGSLTLKSSSNVRVSPNVKFNYYSNLTDLSHCVSGMKKIGELLSTDALKPYKVEDLPGVEGFNILGIPLPKDQTDDAAFETFCRESVASYWHYHGGCLVGKVLDGDFRVTGINALRVVDGSTFPYTPASHPQGFYLMLGRYVGIKILQERSASD

Entity 2 Entity 2 branched

Description description	alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 branched

Description description	alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	570.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 branched

Description description	;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	894.8 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 branched

Description description	;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	748.7 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	benzaldehyde
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	(2R)-hydroxy(phenyl)ethanenitrile
Molecular weight formula_weight	133.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1269

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3gdnA01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	3gdnA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	410 — Cholesterol Oxidase; domain 2
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3gdnB01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	60 — FAD/NAD(P)-binding domain

Domain ID domain_id	3gdnB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	410 — Cholesterol Oxidase; domain 2
Homologous superfamily homologous superfamily	40 —

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Unit-cell length a length_a	68.980 Å
Unit-cell length b length_b	93.790 Å
Unit-cell length c length_c	86.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.47 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.670 Å
Low-resolution limit resolution_low	19.970 Å
R factor r_factor	—
R_work r_work	0.1740
R_free r_free	0.1970

Almond hydroxynitrile lyase in complex with benzaldehyde

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

R-oxynitrile lyase isoenzyme 1

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

3gdn__assembly_1__model_1

3gdn__assembly_1__model_1 | I(q)

3gdn__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)

Almond hydroxynitrile lyase in complex with benzaldehyde

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

R-oxynitrile lyase isoenzyme 1

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

3gdn__assembly_1__model_1

3gdn__assembly_1__model_1 | I(q)

3gdn__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (2)