1vay

Crystal Structure of Uricase from Arthrobacter globiformis with inhibitor 8-azaxanthine

Method: X-RAY DIFFRACTION

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

No usable UniProt protein identity is available for this entry.

The relationship tables retain this entry's assembly and composition data, but cross-PDB links for the same protein cannot be established reliably without a unified protein identity.

Assembly Composition of the Current Entry

Assembly	Physical composition	Protein state	蛋白 / DNA / RNA / 其他Polymer	Data consistency
1	Protein homooligomer	Homooligomer	4 / 0 / 0 / 0	Consistent with protein count
2	Protein homooligomer	Homooligomer	4 / 0 / 0 / 0	Consistent with protein count

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	1vay
Deposition date deposition_date	2004-02-19
Structure title title	Crystal Structure of Uricase from Arthrobacter globiformis with inhibitor 8-azaxanthine
Keywords keywords	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.

1vay__assembly_1__model_1

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

Download this curve (.dat)

1vay__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vay__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.25 Å
Rg (electron density)	29.82 Å
Total Rg	30.61 Å
Atom count	9172
Residues	1148
Excluded volume	160270 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vay__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1vay__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 (3)

Entity 1 Entity 1 polymer

Description description	Uric acid oxidase
Molecular weight formula_weight	32458.0 kDa
EC 编号 ec_number	1.7.3.3
Source method src_method	nat
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	19410

TKVVLGQNQYGKAEVRLVKVTRNTARHEIQDLNVTSQLRGDFEAAHTAGDNAHVVATDTQKNTVYAFARDGFATTEEFLLRLGKHFTEGFDWVTGGRWAAQQFFWDRINDHDHAFSRNKSEVRTAVLEISGSEQAIVAGIEGLTVLKSTGSEFHGFPRDKYTTLQETTDRILATDVSARWRYNTVEVDFDAVYASVRGLLLKAFAETHSLALQQTMYEMGRAVIETHPEIDEIKMSLPNKHHFLVDLQPFGQDNPNEVFYAADRPYGLIEATIQREGSRADHPIWSN

Entity 2 Entity 2 non-polymer

Description description	8-AZAXANTHINE
Molecular weight formula_weight	153.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1066

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d1vaya1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.4 — Urate oxidase (uricase)

Domain ID domain_id	d1vaya2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.4 — Urate oxidase (uricase)

Domain ID domain_id	d1vayb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.4 — Urate oxidase (uricase)

Domain ID domain_id	d1vayb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.4 — Urate oxidase (uricase)

Domain ID domain_id	d1vayc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.4 — Urate oxidase (uricase)

Domain ID domain_id	d1vayc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.4 — Urate oxidase (uricase)

Domain ID domain_id	d1vayd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.4 — Urate oxidase (uricase)

Domain ID domain_id	d1vayd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.4 — Urate oxidase (uricase)

Domain ID domain_id	d1vaye1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.4 — Urate oxidase (uricase)

Domain ID domain_id	d1vaye2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.4 — Urate oxidase (uricase)

Domain ID domain_id	d1vayf1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.4 — Urate oxidase (uricase)

Domain ID domain_id	d1vayf2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.4 — Urate oxidase (uricase)

Domain ID domain_id	d1vayg1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.4 — Urate oxidase (uricase)

Domain ID domain_id	d1vayg2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.4 — Urate oxidase (uricase)

Domain ID domain_id	d1vayh1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.4 — Urate oxidase (uricase)

Domain ID domain_id	d1vayh2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.96 — T-fold
Superfamily Superfamily superfamily	d.96.1 — Tetrahydrobiopterin biosynthesis enzymes-like
Family Family family	d.96.1.4 — Urate oxidase (uricase)

CATH v4.4 (8 domains)

Domain ID domain_id	1vayA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	270 — Urate Oxidase
Homologous superfamily homologous superfamily	10 — Urate Oxidase;

Domain ID domain_id	1vayB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	270 — Urate Oxidase
Homologous superfamily homologous superfamily	10 — Urate Oxidase;

Domain ID domain_id	1vayC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	270 — Urate Oxidase
Homologous superfamily homologous superfamily	10 — Urate Oxidase;

Domain ID domain_id	1vayD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	270 — Urate Oxidase
Homologous superfamily homologous superfamily	10 — Urate Oxidase;

Domain ID domain_id	1vayE00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	270 — Urate Oxidase
Homologous superfamily homologous superfamily	10 — Urate Oxidase;

Domain ID domain_id	1vayF00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	270 — Urate Oxidase
Homologous superfamily homologous superfamily	10 — Urate Oxidase;

Domain ID domain_id	1vayG00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	270 — Urate Oxidase
Homologous superfamily homologous superfamily	10 — Urate Oxidase;

Domain ID domain_id	1vayH00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	270 — Urate Oxidase
Homologous superfamily homologous superfamily	10 — Urate Oxidase;

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Unit-cell length a length_a	83.330 Å
Unit-cell length b length_b	122.280 Å
Unit-cell length c length_c	283.920 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.240 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1970
R_work r_work	0.1970
R_free r_free	0.2420