7zcy

Sporosarcina pasteurii urease (SPU) co-crystallized in the presence of an Ebselen-derivative and bound to Se atoms

Method: X-RAY DIFFRACTION

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

Urease subunit gamma

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Urease subunit beta × 3 （P41021） Urease subunit alpha × 3 （P41020） 1,2-ETHANEDIOL × 60 SULFATE ION × 24 NICKEL (II) ION × 6 HYDROXIDE ION × 3 N-(2-chloranyl-4-fluoranyl-phenyl)-2-selanyl-benzamide × 3 SELENIUM ATOM × 6 water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	URE3_SPOPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–100； UniProt 1–100

Urease subunit beta

OrganismNot specified

UniProt P41021

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Urease subunit gamma × 3 （P41022） Urease subunit alpha × 3 （P41020） 1,2-ETHANEDIOL × 60 SULFATE ION × 24 NICKEL (II) ION × 6 HYDROXIDE ION × 3 N-(2-chloranyl-4-fluoranyl-phenyl)-2-selanyl-benzamide × 3 SELENIUM ATOM × 6 water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	URE2_SPOPA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–122； UniProt 5–126

Urease subunit alpha

OrganismNot specified

UniProt P41020

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 9	Urease subunit gamma × 3 （P41022） Urease subunit beta × 3 （P41021） 1,2-ETHANEDIOL × 60 SULFATE ION × 24 NICKEL (II) ION × 6 HYDROXIDE ION × 3 N-(2-chloranyl-4-fluoranyl-phenyl)-2-selanyl-benzamide × 3 SELENIUM ATOM × 6 water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	URE1_SPOPA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–570； UniProt 1–570

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	7zcy
Deposition date deposition_date	2022-03-29
Structure title title	Sporosarcina pasteurii urease (SPU) co-crystallized in the presence of an Ebselen-derivative and bound to Se atoms
Keywords keywords	urease, nickel, Ebselen, selenium, HYDROLASE; HYDROLASE
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.

7zcy__assembly_1__model_1

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

Download this curve (.dat)

7zcy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7zcy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.58 Å
Rg (electron density)	38.61 Å
Total Rg	39.01 Å
Atom count	18563
Residues	2370
Excluded volume	329650 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7zcy__assembly_1__model_1`	nonameric （9）	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	Urease subunit gamma
Molecular weight formula_weight	11134.9 kDa
EC 编号 ec_number	3.5.1.5
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7282

MHLNPAEKEKLQIFLASELALKRKARGLKLNYPEAVAIITSFIMEGARDGKTVAMLMEEGKHVLTRDDVMEGVPEMIDDIQAEATFPDGTKLVTVHNPIS

Entity 2 Entity 2 polymer

Description description	Urease subunit beta
Molecular weight formula_weight	13529.1 kDa
EC 编号 ec_number	3.5.1.5
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

NYIVPGEYRVAEGEIEINAGREKTTIRVSNTGDRPIQVGSHIHFVEVNKELLFDRAEGIGRRLNIPSGTAARFEPGEEMEVELTELGGNREVFGISDLTNGSVDNKELILQRAKELGYKGVE

Entity 3 Entity 3 polymer

Description description	Urease subunit alpha
Molecular weight formula_weight	61575.6 kDa
EC 编号 ec_number	3.5.1.5
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MKINRQQYAESYGPTVGDQVRLADTDLWIEVEKDYTTYGDEANFGGGKVLREGMGENGTYTRTENVLDLLLTNALILDYTGIYKADIGVKDGYIVGIGKGGNPDIMDGVTPNMIVGTATEVIAAEGKIVTAGGIDTHVHFINPDQVDVALANGITTLFGGGTGPAEGSKATTVTPGPWNIEKMLKSTEGLPINVGILGKGHGSSIAPIMEQIDAGAAGLKIHEDWGATPASIDRSLTVADEADVQVAIHSDTLNEAGFLEDTLRAINGRVIHSFHVEGAGGGHAPDIMAMAGHPNVLPSSTNPTRPFTVNTIDEHLDMLMVCHHLKQNIPEDVAFADSRIRPETIAAEDILHDLGIISMMSTDALAMGRAGEMVLRTWQTADKMKKQRGPLAEEKNGSDNFRAKRYVSKYTINPAIAQGIAHEVGSIEEGKFADLVLWEPKFFGVKADRVIKGGIIAYAQIGDPSASIPTPQPVMGRRMYGTVGDLIHDTNITFMSKSSIQQGVPAKLGLKRRIGTVKNCRNIGKKDMKWNDVTTDIDINPETYEVKVDGEVLTCEPVKELPMAQRYFLF

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	20

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	HYDROXIDE ION
Molecular weight formula_weight	17.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	N-(2-chloranyl-4-fluoranyl-phenyl)-2-selanyl-benzamide
Molecular weight formula_weight	328.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	SELENIUM ATOM
Molecular weight formula_weight	79.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	767

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Unit-cell length a length_a	131.612 Å
Unit-cell length b length_b	131.612 Å
Unit-cell length c length_c	189.003 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 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	1.540 Å
Low-resolution limit resolution_low	97.800 Å
R factor r_factor	0.1386
R_work r_work	0.1375
R_free r_free	0.1599

Sporosarcina pasteurii urease (SPU) co-crystallized in the presence of an Ebselen-derivative and bound to Se atoms

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

Urease subunit gamma

State in the Current Structure

Other States of the Same Protein in the Database

Urease subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Urease subunit alpha

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

7zcy__assembly_1__model_1

7zcy__assembly_1__model_1 | I(q)

7zcy__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 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer 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

7. Citations (1)

Sporosarcina pasteurii urease (SPU) co-crystallized in the presence of an Ebselen-derivative and bound to Se atoms

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

Urease subunit gamma

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Urease subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Urease subunit alpha

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

7zcy__assembly_1__model_1

7zcy__assembly_1__model_1 | I(q)

7zcy__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 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer 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

7. Citations (1)