Structure of PDB 3wom Chain B

Receptor sequence

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

GEGMWVPQQLPEIAGPLKKAGLKLSPQQISDLTGDPMGAVVALGGCTASF
VSPNGLVVTNHHCAYGAIQLNSTAENNLIKNGFNAPTTADEVSAGPNARV
FVLDEITDVTKDAKAAIAAAGDDALARTKALEAFEKKLIADCEAEAGFRC
RLYSFSGGNTYRLFKNLEIKDVRLAYAPPGSVGKFGGDIDNWMWPRHTGD
FAFYRAYVGKDGKPAAFSKDNVPYQPKHWLKFADQPLGAGDFVMVAGYPG
STNRYALAAEFDNTAQWTYPTIARHYKNQIAMVEAAGKQNADIQVKYAAT
MAGWNNTSKNYDGQLEGFKRIDAAGQKLREEAAVLGWLKGQGAKGQPALD
AHAKLLDLLEQSKATRDRDLTLALFNNTAMLGSATQLYRLSIEREKPNAE
RESGYQERDLPAIEGGLKQLERRYVAAMDRQLQEYWLNEYIKLPADQRVA
AVDAWLGGNDAAAVKRALDRLAGTKLGSTEERLKWFAADRKAFEASNDPA
IQYAVAVMPTLLKLEQERKTRAGENLAARPVYLQALADYKKSQGEFVYPD
ANLSLRITFGNVMGYAPKDGMEYTPFTTLEGVVAKETGQDPFDSPKALLD
AVAAKRYGGLEDKRIGSVPVNYLSDLDITGGNSGSPVLDAHGKLVGLAFD
GNWESVSSNWVFDPKMTRMIAVDGRYLRWIMQEVYPAPQLLKEMNVG

3D structure

• PDB: 3wom S46 peptidases are the first exopeptidases to be members of clan PA
• Chain: B
• Resolution: 1.86 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	VAL	B	H86 N215 W216 N330 F673 D674	H62 N191 W192 N306 F649 D650
BS02	TYR	B	W216 I652 T653 G654 S657 D674 G675	W192 I628 T629 G630 S633 D650 G651
BS03	ZN	B	K47 H665	K23 H641
BS04	ZN	B	E505 K508	E481 K484

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