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3ubp

DIAMIDOPHOSPHATE INHIBITED BACILLUS PASTEURII UREASE

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (UREASE GAMMA SUBUNIT)

OrganismNot specified

UniProt P41022

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 PROTEIN (UREASE BETA SUBUNIT) × 1 （P41021） PROTEIN (UREASE ALPHA SUBUNIT) × 1 （P41020） NICKEL (II) ION × 2 DIAMIDOPHOSPHATE × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 9 PROTEIN (UREASE BETA SUBUNIT) × 3 （P41021） PROTEIN (UREASE ALPHA SUBUNIT) × 3 （P41020） NICKEL (II) ION × 6 DIAMIDOPHOSPHATE × 3 water × 9 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1ie7 1ie7 1ie7 1s3t 1ubp 2ubp 2ubp 3ubp 3ubp 4ac7 4ceu 4cex

27 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name URE3_BACPA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–101； UniProt 1–100

PROTEIN (UREASE BETA SUBUNIT)

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 3 PROTEIN (UREASE GAMMA SUBUNIT) × 1 （P41022） PROTEIN (UREASE ALPHA SUBUNIT) × 1 （P41020） NICKEL (II) ION × 2 DIAMIDOPHOSPHATE × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 9 PROTEIN (UREASE GAMMA SUBUNIT) × 3 （P41022） PROTEIN (UREASE ALPHA SUBUNIT) × 3 （P41020） NICKEL (II) ION × 6 DIAMIDOPHOSPHATE × 3 water × 9 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1ie7 1ie7 1ie7 1s3t 1ubp 2ubp 2ubp 3ubp 3ubp 4ac7 4ceu 4cex

40 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name URE2_BACPA
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–126； UniProt 1–126

PROTEIN (UREASE ALPHA SUBUNIT)

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 3 PROTEIN (UREASE GAMMA SUBUNIT) × 1 （P41022） PROTEIN (UREASE BETA SUBUNIT) × 1 （P41021） NICKEL (II) ION × 2 DIAMIDOPHOSPHATE × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 9 PROTEIN (UREASE GAMMA SUBUNIT) × 3 （P41022） PROTEIN (UREASE BETA SUBUNIT) × 3 （P41021） NICKEL (II) ION × 6 DIAMIDOPHOSPHATE × 3 water × 9 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1ie7 1ie7 1ie7 1s3t 1ubp 2ubp 2ubp 3ubp 3ubp 4ac7 4ceu 4cex

27 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name URE1_BACPA
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–570； UniProt 1–569

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_id3ubp
Deposition date deposition_date1998-12-16
Structure title titleDIAMIDOPHOSPHATE INHIBITED BACILLUS PASTEURII UREASE
Keywords keywordsUREASE, BACILLUS PASTEURII, NICKEL, DIAMIDOPHOSPHATE, METALLOENZYME, HYDROLASE; HYDROLASE
Experimental Method methodX-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.

3ubp__assembly_1__model_1

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

Download this curve (.dat)

3ubp__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3ubp__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）30.09 Å
Rg (electron density)29.35 Å
Total Rg29.94 Å
Atom count6062
Residues791
Excluded volume107700 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3ubp__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3ubp__assembly_2__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 (6)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3ubpa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.8 — Urease, gamma-subunit
Superfamily Superfamily superfamilyd.8.1 — Urease, gamma-subunit
Family Family familyd.8.1.1 — Urease, gamma-subunit
Domain ID domain_idd3ubpb_
Class classb — All beta proteins
Fold Fold foldb.85 — beta-clip
Superfamily Superfamily superfamilyb.85.3 — Urease, beta-subunit
Family Family familyb.85.3.1 — Urease, beta-subunit
Domain ID domain_idd3ubpc1
Class classb — All beta proteins
Fold Fold foldb.92 — Composite domain of metallo-dependent hydrolases
Superfamily Superfamily superfamilyb.92.1 — Composite domain of metallo-dependent hydrolases
Family Family familyb.92.1.1 — alpha-Subunit of urease
Domain ID domain_idd3ubpc2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
Family Family familyc.1.9.2 — alpha-subunit of urease, catalytic domain

CATH v4.4 (4 domains)

Domain ID domain_id3ubpA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology280 — Urease; subunit A
Homologous superfamily homologous superfamily10 — Urease, gamma-like subunit
Domain ID domain_id3ubpB00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology150 — Urease, subunit B
Homologous superfamily homologous superfamily10 — Urease, beta subunit
Domain ID domain_id3ubpC01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology40 — Urease, subunit C; domain 1
Homologous superfamily homologous superfamily10 — Urease, subunit C, domain 1
Domain ID domain_id3ubpC02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily140 — Metal-dependent hydrolases
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7. Citations (5)