Structure of PDB 1d3v Chain B Binding Site BS01

Receptor Information

>1d3v Chain B (length=308) Species: 10116 (Rattus norvegicus)

KPIEIIGAPFSKGQPRGGVEKGPAALRKAGLVEKLKETEYNVRDHGDLAF
VDVPNDSPFQIVKNPRSVGKANEQLAAVVAETQKNGTISVVLGGDHSMAI
GSISGHARVHPDLCVIWVDAHTDINTPLTTSSGNLHGQPVAFLLKELKGK
FPDVPGFSWVTPCISAKDIVYIGLRDVDPGEHYIIKTLGIKYFSMTEVDK
LGIGKVMEETFSYLLGRKKRPIHLSFDVDGLDPVFTPATGTPVVGGLSYR
EGLYITEEIYKTGLLSGLDIMEVNPTLGKTPEEVTRTVNTAVALTLSCFG
TKREGNHK

Ligand information

• Ligand ID: MN
• InChI: InChI=1S/Mn/q+2
• InChIKey: WAEMQWOKJMHJLA-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mn+2]
  CACTVS 3.341: [Mn++]
• Formula: Mn
• Name: MANGANESE (II) ION
• DrugBank: DB06757
• PDB chain: 1d3v Chain B Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1d3v Arginase-boronic acid complex highlights a physiological role in erectile function.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): H101 D124 D128 D232
• Binding residue (residue number reindexed from 1): H96 D119 D123 D227
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H101 D124 H126 D128 H141 D232 D234 E277
• Catalytic site (residue number reindexed from 1): H96 D119 H121 D123 H136 D227 D229 E272
• Enzyme Commision number: 3.5.3.1: arginase.

Gene Ontology

Molecular Function

• GO:0004053 arginase activity
• GO:0016787 hydrolase activity
• GO:0016813 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines
• GO:0030145 manganese ion binding
• GO:0042802 identical protein binding
• GO:0046872 metal ion binding

Biological Process

• GO:0000050 urea cycle
• GO:0001889 liver development
• GO:0001938 positive regulation of endothelial cell proliferation
• GO:0002250 adaptive immune response
• GO:0006525 arginine metabolic process
• GO:0007565 female pregnancy
• GO:0009410 response to xenobiotic stimulus
• GO:0009635 response to herbicide
• GO:0010042 response to manganese ion
• GO:0010043 response to zinc ion
• GO:0010269 response to selenium ion
• GO:0014075 response to amine
• GO:0019547 arginine catabolic process to ornithine
• GO:0030324 lung development
• GO:0032496 response to lipopolysaccharide
• GO:0032964 collagen biosynthetic process
• GO:0033189 response to vitamin A
• GO:0033197 response to vitamin E
• GO:0042130 negative regulation of T cell proliferation
• GO:0042832 defense response to protozoan
• GO:0043200 response to amino acid
• GO:0043434 response to peptide hormone
• GO:0045087 innate immune response
• GO:0046007 negative regulation of activated T cell proliferation
• GO:0046686 response to cadmium ion
• GO:0048545 response to steroid hormone
• GO:0048678 response to axon injury
• GO:0051597 response to methylmercury
• GO:0060056 mammary gland involution
• GO:0060135 maternal process involved in female pregnancy
• GO:0060336 negative regulation of type II interferon-mediated signaling pathway
• GO:0070301 cellular response to hydrogen peroxide
• GO:0070965 positive regulation of neutrophil mediated killing of fungus
• GO:0071222 cellular response to lipopolysaccharide
• GO:0071353 cellular response to interleukin-4
• GO:0071377 cellular response to glucagon stimulus
• GO:0071549 cellular response to dexamethasone stimulus
• GO:0071560 cellular response to transforming growth factor beta stimulus
• GO:1905541 regulation of L-arginine import across plasma membrane
• GO:2000552 negative regulation of T-helper 2 cell cytokine production

Cellular Component

• GO:0005615 extracellular space
• GO:0005737 cytoplasm
• GO:0005741 mitochondrial outer membrane
• GO:0005829 cytosol
• GO:0043025 neuronal cell body

External links

• PDB: RCSB:1d3v, PDBe:1d3v, PDBj:1d3v
• PDBsum: 1d3v
• PubMed: 10542097
• UniProt: P07824|ARGI1_RAT Arginase-1 (Gene Name=Arg1)