Structure of PDB 6udo Chain B

Receptor sequence

>6udoB (length=487) Species: 9606 (Homo sapiens)

YVPDDGLTAQQLFNCGDGLTYNDFLILPGYIDFTADQVDLTSALTKKITL
KTPLVSSPMDTVTEAGMAIAMALTGGIGFIHHNCTPEFQANEVRKVKKYE
QGFITDPVVLSPKDRVRDVFEAKARHGFCGIPITDTGRMGSRLVGIISSR
DIDFLKEEEHDCFLEEIMTKREDLVVAPAGITLKEANEILQRSKKGKLPI
VNEDDELVAIIARTDLKKNRDYPLASKDAKKQLLCGAAIGTHEDDKYRLD
LLAQAGVDVVVLDSSQGNSIFQINMIKYIKDKYPNLQVIGGNVVTAAQAK
NLIDAGVDALRVGMGSGSICITQEVLACGRPQATAVYKVSEYARRFGVPV
IADGGIQNVGHIAKALALGASTVMMGSLLAATTEAPGEYFFSDGIRLKKY
RGMGSLDAMIKVAQGVSGAVQDKGSIHKFVPYLIAGIQHSCQDIGAKSLT
QVRAMMYSGELKFEKRTSSAQVEGGVHSLHSYEKRLF

3D structure

• PDB: 6udo Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation.
• Chain: B
• Resolution: 3.21 Å

Enzymatic activity

• Enzyme Commision number: 1.1.1.205: IMP dehydrogenase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	peptide	B	A54 K57 T477 R480	A43 K46 T450 R453
BS02	IMP	B	S68 M70 R322 G328 S329 I330 C331 D364 G365 G387 S388 M414 G415 Q441	S57 M59 R311 G317 S318 I319 C320 D353 G354 G376 S377 M403 G404 Q414
BS03	GTP	B	I115 P118 F139 C140 G141 S159 S160 K208 A223 T225	I104 P107 F128 C129 G130 S148 S149 K197 A212 T214
BS04	GTP	B	L194 K195 N198 D226 L227 N230 K242	L183 K184 N187 D215 L216 N219 K231
BS05	ATP	B	S159 S160 R161 D162 L185 V186 K206 K208	S148 S149 R150 D151 L174 V175 K195 K197

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003677 DNA binding
• GO:0003723 RNA binding
• GO:0003824 catalytic activity
• GO:0003938 IMP dehydrogenase activity
• GO:0005515 protein binding
• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006164 purine nucleotide biosynthetic process
• GO:0006177 GMP biosynthetic process
• GO:0006183 GTP biosynthetic process
• GO:0007623 circadian rhythm
• GO:0046651 lymphocyte proliferation
• GO:0071353 cellular response to interleukin-4
• GO:0097294 'de novo' XMP biosynthetic process

Cellular Component

• GO:0005576 extracellular region
• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005778 peroxisomal membrane
• GO:0005829 cytosol
• GO:0016020 membrane
• GO:0034774 secretory granule lumen
• GO:0070062 extracellular exosome
• GO:1904813 ficolin-1-rich granule lumen

External links

• PDB: RCSB:6udo, PDBe:6udo, PDBj:6udo
• PDBsum: 6udo
• PubMed: 31999252
• UniProt: P12268|IMDH2_HUMAN Inosine-5'-monophosphate dehydrogenase 2 (Gene Name=IMPDH2)