Structure of PDB 3wor Chain B

Receptor sequence

>3worB (length=697) Species: 128785 (Pseudoxanthomonas mexicana)

GEGMWVPQQLPEIAGPLKKAGLKLSPQQISDLTGDPMGAVVALGGCTASF
VSPNGLVVTNHACAYGAIQLNSTAENNLIKNGFNAPTTADEVSAGPNARV
FVLDEITDVTKDAKAAIAAAGDDALARTKALEAFEKKLIADCEAEAGFRC
RLYSFSGGNTYRLFKNLEIKDVRLAYAPPGSVGKFGGDIDNWMWPRHTGA
FAFYRAYVGKDGKPAAFSKDNVPYQPKHWLKFADQPLGAGDFVMVAGYPG
STNRYALAAEFDNTAQWTYPTIARHYKNQIAMVEAAGKQNADIQVKYAAT
MAGWNNTSKNYDGQLEGFKRIDAAGQKLREEAAVLGWLKGQGAKGQPALD
AHAKLLDLLEQSKATRDRDLTLALFNNTAMLGSATQLYRLSIEREKPNAE
RESGYQERDLPAIEGGLKQLERRYVAAMDRQLQEYWLNEYIKLPADQRVA
AVDAWLGGNDAAAVKRALDRLAGTKLGSTEERLKWFAADRKAFEASNDPA
IQYAVAVMPTLLKLEQERKTRAGENLAARPVYLQALADYKKSQGEFVYPD
ANLSLRITFGNVMGYAPKDGMEYTPFTTLEGVVAKETGQDPFDSPKALLD
AVAAKRYGGLEDKRIGSVPVNYLSDLDITGGNAGSPVLDAHGKLVGLAFD
GNWESVSSNWVFDPKMTRMIAVDGRYLRWIMQEVYPAPQLLKEMNVG

3D structure

• PDB: 3wor S46 peptidases are the first exopeptidases to be members of clan PA
• Chain: B
• Resolution: 2.1 Å

Enzymatic activity

• Enzyme Commision number: 3.4.14.-

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	G69 N215 W216 G274 N330 I652 T653 G654 G655 A657 F673 D674	G45 N191 W192 G250 N306 I628 T629 G630 G631 A633 F649 D650
BS02	ZN	B	E505 K508	E481 K484
BS03	ZN	B	K47 H665	K23 H641

Gene Ontology

Molecular Function

• GO:0004175 endopeptidase activity
• GO:0004177 aminopeptidase activity
• GO:0008239 dipeptidyl-peptidase activity
• GO:0042802 identical protein binding
• GO:0042803 protein homodimerization activity
• GO:0070009 serine-type aminopeptidase activity

Biological Process

• GO:0006508 proteolysis
• GO:0009056 catabolic process
• GO:0051603 proteolysis involved in protein catabolic process

External links

• PDB: RCSB:3wor, PDBe:3wor, PDBj:3wor
• PDBsum: 3wor
• PubMed: 24827749
• UniProt: V5YM14|DAPB2_PSEMX Dipeptidyl aminopeptidase BII (Gene Name=dapb2)