Structure of PDB 3pkb Chain A

Receptor sequence

>3pkbA (length=284) Species: 1773 (Mycobacterium tuberculosis)

PSRTALSPGVLSPTRPVPNWIARPEYVGKPAAQEGSEPWVQTPEVIEKMR
VAGRIAAGALAEAGKAVAPGVTTDELDRIAHEYLVDNGAYPSTLGYKGFP
KSCCTSLNEVICHGIPDSTVITDGDIVNIDVTAYIGGVHGDTNATFPAGD
VADEHRLLVDRTREATMRAINTVKPGRALSVIGRVIESYANRFGYNVVRD
FTGHGIGTTFHNGLVVLHYDQPAVETIMQPGMTFTIEPMINLGALDYEIW
DDGWTVVTKDRKWTAQFEHTLLVTDTGVEILTCL

3D structure

• PDB: 3pkb Inhibition of Mycobacterium tuberculosis Methionine Aminopeptidases by Bengamide Derivatives.
• Chain: A
• Resolution: 1.25 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H114 D131 D142 G204 H205 G208 H212 L215 E238 N242 E269
• Catalytic site (residue number reindexed from 1): H113 D130 D141 G203 H204 G207 H211 L214 E237 N241 E268
• Enzyme Commision number: 3.4.11.18: methionyl aminopeptidase.

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	Y16	A	Y97 H114 D131 D142 F202 T203 H205 H212 E238 E269	Y96 H113 D130 D141 F201 T202 H204 H211 E237 E268	MOAD: ic50=0.62uM PDBbind-CN: -logKd/Ki=6.21,IC50=620nM
BS02	MN	A	D142 H205 T236 E238 E269	D141 H204 T235 E237 E268
BS03	MN	A	D131 D142 E269	D130 D141 E268

Gene Ontology

Molecular Function

• GO:0004177 aminopeptidase activity
• GO:0004239 initiator methionyl aminopeptidase activity
• GO:0005506 iron ion binding
• GO:0008235 metalloexopeptidase activity
• GO:0046872 metal ion binding
• GO:0046914 transition metal ion binding
• GO:0050897 cobalt ion binding
• GO:0070006 metalloaminopeptidase activity

Biological Process

• GO:0006508 proteolysis
• GO:0016485 protein processing

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:3pkb, PDBe:3pkb, PDBj:3pkb
• PDBsum: 3pkb
• PubMed: 21465667
• UniProt: P9WK19|MAP12_MYCTU Methionine aminopeptidase 2 (Gene Name=map)