Structure of PDB 4ehm Chain B

Receptor sequence

>4ehmB (length=325) Species: 10116 (Rattus norvegicus)

QKDVTIKSDAPDTLLLEKHADYIASYGSDDYEYCMSEYLRMSGVYWGLTV
MDLMGQLHRMNKEEILVFIKSCQHECGGVSASIGHDPHLLYTLSAVQILT
LYDSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAVATLALL
GKLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQ
LHQVNSDLLGWWLCERQLPSGGLNGRPEKLPDVCYSWWVLASLKIIGRLH
WIDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSLLGEEQI
KPVSPVFCMPEEVLQRVNVQPELVS

3D structure

• PDB: 4ehm Psoromic Acid is a Selective and Covalent Rab-Prenylation Inhibitor Targeting Autoinhibited RabGGTase
• Chain: B
• Resolution: 2.2 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H190 R232 K235 D238 C240 Y241 D280 D287 H290
• Catalytic site (residue number reindexed from 1): H184 R226 K229 D232 C234 Y235 D274 D281 H284
• Enzyme Commision number: 2.5.1.60: protein geranylgeranyltransferase type II.

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	PJA	B	R144 G192 Q193 W244 F289	R138 G186 Q187 W238 F283	PDBbind-CN: -logKd/Ki=5.85,IC50=1.4uM
BS02	ZN	B	D238 C240 H290	D232 C234 H284
BS03	CA	B	H64 M66	H58 M60

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004659 prenyltransferase activity
• GO:0004661 protein geranylgeranyltransferase activity
• GO:0004663 Rab geranylgeranyltransferase activity
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0008318 protein prenyltransferase activity
• GO:0019840 isoprenoid binding
• GO:0031267 small GTPase binding
• GO:0046872 metal ion binding

Biological Process

• GO:0018344 protein geranylgeranylation

Cellular Component

• GO:0005968 Rab-protein geranylgeranyltransferase complex

External links

• PDB: RCSB:4ehm, PDBe:4ehm, PDBj:4ehm
• PDBsum: 4ehm
• PubMed: 22480322
• UniProt: Q08603|PGTB2_RAT Geranylgeranyl transferase type-2 subunit beta (Gene Name=Rabggtb)