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4ixu

Crystal structure of human Arginase-2 complexed with inhibitor 11d: {(5R)-5-amino-5-carboxy-5-[(3-endo)-8-(3,4-dichlorobenzyl)-8-azabicyclo[3.2.1]oct-3-yl]pentyl}(trihydroxy)borate(1-)

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

Arginase-2, mitochondrial

Homo sapiens

UniProt P78540

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 MANGANESE (II) ION × 2 BENZAMIDINE × 1 BETA-MERCAPTOETHANOL × 2 {(5R)-5-amino-5-carboxy-5-[(3-endo)-8-(3,4-dichlorobenzyl)-8-azabicyclo[3.2.1]oct-3-yl]pentyl}(trihydroxy)borate(1-) × 1 water × 1 Consistent with protein count
2 Protein monomer Monomer Protein 1 MANGANESE (II) ION × 2 BENZAMIDINE × 1 BETA-MERCAPTOETHANOL × 2 {(5R)-5-amino-5-carboxy-5-[(3-endo)-8-(3,4-dichlorobenzyl)-8-azabicyclo[3.2.1]oct-3-yl]pentyl}(trihydroxy)borate(1-) × 1 water × 1 Consistent with protein count
3 Protein monomer Monomer Protein 1 MANGANESE (II) ION × 2 BENZAMIDINE × 1 BETA-MERCAPTOETHANOL × 2 {(5R)-5-amino-5-carboxy-5-[(3-endo)-8-(3,4-dichlorobenzyl)-8-azabicyclo[3.2.1]oct-3-yl]pentyl}(trihydroxy)borate(1-) × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
4hze 4hze 4i06 4i06 4i06 4ie2 4ie2 4ie2 4ie3 4ie3 4ie3 4ixu

17 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers
1pq3 1pq3 4hze 4i06 4ie2 4ie3 4ixv 6q37 6q39 8rfa 8rg6 8rgf

15 assemblies; showing the first 12

Heteromeric or nucleic-acid complex
6ss2 6ss4 6ss6

3 assemblies

View Construct and Data Evidence
UniProt name ARGI2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–306； UniProt 24–329 Author chain B； PDBConstruct 1–306； UniProt 24–329 Author chain C； PDBConstruct 1–306； UniProt 24–329

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_id4ixu
Deposition date deposition_date2013-01-28
Structure title titleCrystal structure of human Arginase-2 complexed with inhibitor 11d: {(5R)-5-amino-5-carboxy-5-[(3-endo)-8-(3,4-dichlorobenzyl)-8-azabicyclo[3.2.1]oct-3-yl]pentyl}(trihydroxy)borate(1-)
Keywords keywords;metalloenzyme, alpha/beta fold, Hydrolase, Arginine metabolism, Manganese, boronate, Mitochondrion, HYDROLASE-HYDROLASE INHIBITOR complex ;; HYDROLASE/HYDROLASE INHIBITOR
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.

4ixu__assembly_1__model_1

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

Download this curve (.dat)

4ixu__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

4ixu__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）19.03 Å
Rg (electron density)17.78 Å
Total Rg18.76 Å
Atom count2378
Residues306
Excluded volume42335 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4ixu__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4ixu__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 4ixu__assembly_3__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 (6)

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd4ixua_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.42 — Arginase/deacetylase
Superfamily Superfamily superfamilyc.42.1 — Arginase/deacetylase
Family Family familyc.42.1.1 — Arginase-like amidino hydrolases
Domain ID domain_idd4ixub_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.42 — Arginase/deacetylase
Superfamily Superfamily superfamilyc.42.1 — Arginase/deacetylase
Family Family familyc.42.1.1 — Arginase-like amidino hydrolases
Domain ID domain_idd4ixuc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.42 — Arginase/deacetylase
Superfamily Superfamily superfamilyc.42.1 — Arginase/deacetylase
Family Family familyc.42.1.1 — Arginase-like amidino hydrolases

CATH v4.4 (3 domains)

Domain ID domain_id4ixuA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology800 — Arginase; Chain A
Homologous superfamily homologous superfamily10 — Ureohydrolase domain
Domain ID domain_id4ixuB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology800 — Arginase; Chain A
Homologous superfamily homologous superfamily10 — Ureohydrolase domain
Domain ID domain_id4ixuC00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology800 — Arginase; Chain A
Homologous superfamily homologous superfamily10 — Ureohydrolase domain
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7. Citations (1)