1ryi

STRUCTURE OF GLYCINE OXIDASE WITH BOUND INHIBITOR GLYCOLATE

Method: X-RAY DIFFRACTION

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

GLYCINE OXIDASE

Bacillus subtilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	FLAVIN-ADENINE DINUCLEOTIDE × 4 GLYCOLIC ACID × 4 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	FLAVIN-ADENINE DINUCLEOTIDE × 4 GLYCOLIC ACID × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLOX_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 14–382； UniProt 1–369 Author chain B； PDBConstruct 14–382； UniProt 1–369 Author chain C； PDBConstruct 14–382； UniProt 1–369 Author chain D； PDBConstruct 14–382； UniProt 1–369

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	1ryi
Deposition date deposition_date	2003-12-22
Structure title title	STRUCTURE OF GLYCINE OXIDASE WITH BOUND INHIBITOR GLYCOLATE
Keywords keywords	FLAVOPROTEIN; OXIDASE; PROTEIN-INHIBITOR 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.

1ryi__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1ryi__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ryi__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	34.65 Å
Rg (electron density)	33.63 Å
Total Rg	34.14 Å
Atom count	11608
Residues	1456
Excluded volume	205940 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ryi__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ryi__assembly_2__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	GLYCINE OXIDASE
Molecular weight formula_weight	42636.7 kDa
EC 编号 ec_number	1.4.3.19
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	12720

MHHHHHHMARIRAMKRHYEAVVIGGGIIGSAIAYYLAKENKNTALFESGTMGGRTTSAAAGMLGAHAECEERDAFFDFAMHSQRLYKGLGEELYALSGVDIRQHNGGMFKLAFSEEDVLQLRQMDDLDSVSWYSKEEVLEKEPYASGDIFGASFIQDDVHVEPYFVCKAYVKAAKMLGAEIFEHTPVLHVERDGEALFIKTPSGDVWANHVVVASGVWSGMFFKQLGLNNAFLPVKGECLSVWNDDIPLTKTLYHDHCYIVPRKSGRLVVGATMKPGDWSETPDLGGLESVMKKAKTMLPAIQNMKVDRFWAGLRPGTKDGKPYIGRHPEDSRILFAAGHFRNGILLAPATGALISDLIMNKEVNQDWLHAFRIDRKEAVNI

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	GLYCOLIC ACID
Molecular weight formula_weight	76.1 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	1046

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1ryia1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

Domain ID domain_id	d1ryia2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
Family Family family	d.16.1.3 — D-aminoacid oxidase-like

Domain ID domain_id	d1ryib1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

Domain ID domain_id	d1ryib2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
Family Family family	d.16.1.3 — D-aminoacid oxidase-like

Domain ID domain_id	d1ryic1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

Domain ID domain_id	d1ryic2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
Family Family family	d.16.1.3 — D-aminoacid oxidase-like

Domain ID domain_id	d1ryid1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

Domain ID domain_id	d1ryid2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
Family Family family	d.16.1.3 — D-aminoacid oxidase-like

CATH v4.4 (8 domains)

Domain ID domain_id	1ryiA01
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	1ryiA02
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

Domain ID domain_id	1ryiB01
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	1ryiB02
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

Domain ID domain_id	1ryiC01
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	1ryiC02
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

Domain ID domain_id	1ryiD01
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	1ryiD02
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	73.713 Å
Unit-cell length b length_b	218.765 Å
Unit-cell length c length_c	217.800 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	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	19.920 Å
R factor r_factor	0.1788
R_work r_work	0.1770
R_free r_free	0.2140

STRUCTURE OF GLYCINE OXIDASE WITH BOUND INHIBITOR GLYCOLATE

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

GLYCINE 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

1ryi__assembly_2__model_1

1ryi__assembly_2__model_1 | I(q)

1ryi__assembly_2__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

STRUCTURE OF GLYCINE OXIDASE WITH BOUND INHIBITOR GLYCOLATE

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

GLYCINE 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

1ryi__assembly_2__model_1

1ryi__assembly_2__model_1 | I(q)

1ryi__assembly_2__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)