Structure of PDB 4k7d Chain B

Receptor sequence

>4k7dB (length=312) Species: 10116 (Rattus norvegicus)

SPTYHSFFVYCKGPCHKVQPGKLRVQCGTCRQATLTLAQGPSCWDDVLIP
NRMSGECQSPDCPGTRAEFFFKCGAHPTSDKDTSVALNLITNNSRSIPCI
ACTDVRNPVLVFQCNHRHVICLDCFHLYCVTRLNDRQFVHDAQLGYSLPC
VAGCPNSLIKELHHFRILGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGA
GLLPEQGQRKVTCEGGNGLGCGFVFCRDCKEAYHEGECDSMFEASVDQRA
AEQARWEEKKTTKPCPRCNVPIEKNGGCMHMKCPQPQCKLEWCWNCGCEW
NRACMGDHWFDV

3D structure

• PDB: 4k7d Structure of parkin reveals mechanisms for ubiquitin ligase activation.
• Chain: B
• Resolution: 2.8 Å

Enzymatic activity

• Enzyme Commision number: 2.3.2.31: RBR-type E3 ubiquitin transferase.

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	ZN	B	C150 C154 C212 H215	C11 C15 C73 H76
BS02	ZN	B	C166 C169 C196 C201	C27 C30 C57 C62
BS03	ZN	B	C238 C241 C260 C263	C99 C102 C121 C124
BS04	ZN	B	C253 H257 C289 C293	C114 H118 C150 C154
BS05	ZN	B	C332 C337 C352 C360	C193 C198 C213 C221
BS06	ZN	B	C365 C368 H373 C377	C226 C229 H234 C238
BS07	ZN	B	C418 C421 C436 C441	C265 C268 C283 C288
BS08	ZN	B	C446 C449 C457 H461	C293 C296 C304 H308

Gene Ontology

Molecular Function

• GO:0004842 ubiquitin-protein transferase activity
• GO:0008270 zinc ion binding

Biological Process

• GO:0016567 protein ubiquitination

Cellular Component

• GO:0005739 mitochondrion
• GO:0005829 cytosol

External links

• PDB: RCSB:4k7d, PDBe:4k7d, PDBj:4k7d
• PDBsum: 4k7d
• PubMed: 23661642
• UniProt: Q9JK66|PRKN_RAT E3 ubiquitin-protein ligase parkin (Gene Name=Prkn)