Structure of PDB 5nfn Chain D Binding Site BS01

Receptor Information

>5nfn Chain D (length=318) Species: 9606 (Homo sapiens)

SHMAEAALEAVRSELREFPAAARELCVPLAVPYLDKPPTPLHFYRDWVCP
NRPCIIRNALQHWPALQKWSLPYFRATVGSTEVSVAVTPDGYADAVRGDR
FMMPAERRLPLSFVLDVLEGRAQHPGVLYVQKQCSNLPSELPQLLPDLES
HVPWASEALGKMPDAVNFWLGEAAAVTSLHKDHYENLYCVVSGEKHFLFH
PPSDRPFIPYELYTPATYQLTEEGTFKVVDEEAMEKVPWIPLDPLAPDLA
RYPSYSQAQALRCTVRAGEMLYLPALWFHHVQQSQGCIAVNFWYDMEYDL
KYSYFQLLDSLTKASGLD

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: 5nfn Chain D Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5nfn (3S)-Lysyl hydroxylation of TRAFAC GTPases is catalyzed by the human Jumonji-C oxygenase JMJD7.
• Resolution: 2.982 Å
• Binding residue (original residue number in PDB): H178 D180 H277
• Binding residue (residue number reindexed from 1): H180 D182 H279
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 1.14.11.63: peptidyl-lysine (3S)-dioxygenase.
  3.4.-.-

Gene Ontology

Molecular Function

• GO:0004175 endopeptidase activity
• GO:0004177 aminopeptidase activity
• GO:0004497 monooxygenase activity
• GO:0005515 protein binding
• GO:0016706 2-oxoglutarate-dependent dioxygenase activity
• GO:0035064 methylated histone binding
• GO:0046872 metal ion binding
• GO:0106155 peptidyl-lysine 3-dioxygenase activity

Biological Process

• GO:0006508 proteolysis
• GO:0018126 protein hydroxylation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:5nfn, PDBe:5nfn, PDBj:5nfn
• PDBsum: 5nfn
• UniProt: P0C870|JMJD7_HUMAN Bifunctional peptidase and (3S)-lysyl hydroxylase JMJD7 (Gene Name=JMJD7)