1y56

Crystal structure of L-proline dehydrogenase from P.horikoshii

Method: X-RAY DIFFRACTION

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

hypothetical protein PH1363

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	sarcosine oxidase × 4 （Q5R1N3） FE (III) ION × 4 SULFATE ION × 4 FLAVIN MONONUCLEOTIDE × 4 ADENOSINE-5'-TRIPHOSPHATE × 4 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 4 CHLORIDE ION × 4 FLAVIN-ADENINE DINUCLEOTIDE × 4 water × 8	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	sarcosine oxidase × 1 （Q5R1N3） FE (III) ION × 1 SULFATE ION × 1 FLAVIN MONONUCLEOTIDE × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 1 CHLORIDE ION × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 water × 2	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	FE (III) ION × 1 SULFATE ION × 1 FLAVIN MONONUCLEOTIDE × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O59088_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–493； UniProt 3–495

sarcosine oxidase

Pyrococcus horikoshii

UniProt Q5R1N3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	hypothetical protein PH1363 × 4 （O59088） FE (III) ION × 4 SULFATE ION × 4 FLAVIN MONONUCLEOTIDE × 4 ADENOSINE-5'-TRIPHOSPHATE × 4 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 4 CHLORIDE ION × 4 FLAVIN-ADENINE DINUCLEOTIDE × 4 water × 8	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	hypothetical protein PH1363 × 1 （O59088） FE (III) ION × 1 SULFATE ION × 1 FLAVIN MONONUCLEOTIDE × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 1 CHLORIDE ION × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 water × 2	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	CHLORIDE ION × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5R1N3_PYRHO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–382； UniProt 1–382

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	1y56
Deposition date deposition_date	2004-12-02
Structure title title	Crystal structure of L-proline dehydrogenase from P.horikoshii
Keywords keywords	dehydrogenase, protein-protein complex, OXIDOREDUCTASE; 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.

1y56__assembly_1__model_1

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

Download this curve (.dat)

1y56__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1y56__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	48.66 Å
Rg (electron density)	48.21 Å
Total Rg	48.43 Å
Atom count	27764
Residues	3432
Excluded volume	498070 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1y56__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1y56__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1y56__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1y56__assembly_4__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	hypothetical protein PH1363
Molecular weight formula_weight	55639.2 kDa
EC 编号 ec_number	1.5.99.8
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7147

MLMRPLDLTEKRGKKVTIYFEGKELEAYEGEKLPVALLANEIYWLTTSNEGRKRGAFTFGPVPMTVNGVKGLEARRIKVKDGMKIERQGYYDFHEEPVVEPGEIERVVVDVAIIGGGPAGIGAALELQQYLTVALIEERGWLGGDMWLKGIKQEGFNKDSRKVVEELVGKLNENTKIYLETSALGVFDKGEYFLVPVVRGDKLIEILAKRVVLATGAIDSTMLFENNDMPGVFRRDFALEVMNVWEVAPGRKVAVTGSKADEVIQELERWGIDYVHIPNVKRVEGNEKVERVIDMNNHEYKVDALIFADGRRPDINPITQAGGKLRFRRGYYSPVLDEYHRIKDGIYVAGSAVSIKPHYANYLEGKLVGAYILKEFGYDAQPCIYEEKLREYEPESLSIPRIPLDKFNLEDVQICGCDVSLKKVDEVIRKGITDLQIIKRLTHLAMGFCQGRYCLFNGAVVVSQRTGKKLSEIDLPVARSPIKNVKMGILARR

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	70601
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	sarcosine oxidase
Molecular weight formula_weight	42737.1 kDa
EC 编号 ec_number	1.5.99.8
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MLPEKSEIVVIGGGIVGVTIAHELAKRGEEVTVIEKRFIGSGSTFRCGTGIRQQFNDEANVRVMKRSVELWKKYSEEYGFSFKQTGYLFLLYDDEEVKTFKRNIEIQNKFGVPTKLITPEEAKEIVPLLDISEVIAASWNPTDGKADPFEATTAFAVKAKEYGAKLLEYTEVKGFLIENNEIKGVKTNKGIIKTGIVVNATNAWANLINAMAGIKTKIPIEPYKHQAVITQPIKRGTINPMVISFKYGHAYLTQTFHGGIIGGIGYEIGPTYDLTPTYEFLREVSYYFTKIIPALKNLLILRTWAGYYAKTPDSNPAIGRIEELNDYYIAAGFSGHGFMMAPAVGEMVAELITKGKTKLPVEWYDPYRFERGELRTAALQMG

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	70601
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
Molecular weight formula_weight	221.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	206

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6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	1y56A01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	440 — 2Fe-2S iron-sulphur cluster binding domain, sarcosine oxidase, alpha subunit, N-terminal domain

Domain ID domain_id	1y56A02
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	1y56A04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1100 — BFD-like [2Fe-2S]-binding domain

Domain ID domain_id	1y56B01
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	1y56B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	9 — D-Amino Acid Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — D-Amino Acid Oxidase, subunit A, domain 2

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Unit-cell length a length_a	172.219 Å
Unit-cell length b length_b	172.219 Å
Unit-cell length c length_c	175.398 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 64 2 2
Space-group number int_tables_number	181
Crystal system crystal_system	—

Resolution resolution	2.860 Å
Low-resolution limit resolution_low	19.850 Å
R factor r_factor	0.1840
R_work r_work	0.1817
R_free r_free	0.2256

Crystal structure of L-proline dehydrogenase from P.horikoshii

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

hypothetical protein PH1363

State in the Current Structure

Other States of the Same Protein in the Database

sarcosine oxidase

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

1y56__assembly_1__model_1

1y56__assembly_1__model_1 | I(q)

1y56__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

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) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)

Crystal structure of L-proline dehydrogenase from P.horikoshii

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

hypothetical protein PH1363

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

sarcosine oxidase

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

1y56__assembly_1__model_1

1y56__assembly_1__model_1 | I(q)

1y56__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

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) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)