Structure of PDB 3pkd Chain A

Receptor sequence

>3pkdA (length=282) Species: 1773 (Mycobacterium tuberculosis)

RTALSPGVLSPTRPVPNWIARPEYVGKPAAQEGSEPWVQTPEVIEKMRVA
GRIAAGALAEAGKAVAPGVTTDELDRIAHEYLVDNGAYPSTLGYKGFPKS
CCTSLNEVICHGIPDSTVITDGDIVNIDVTAYIGGVHGDTNATFPAGDVA
DEHRLLVDRTREATMRAINTVKPGRALSVIGRVIESYANRFGYNVVRDFT
GHGIGTTFHNGLVVLHYDQPAVETIMQPGMTFTIEPMINLGALDYEIWDD
GWTVVTKDRKWTAQFEHTLLVTDTGVEILTCL

3D structure

• PDB: 3pkd Inhibition of Mycobacterium tuberculosis Methionine Aminopeptidases by Bengamide Derivatives.
• Chain: A
• Resolution: 1.47 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): H111 D128 D139 G201 H202 G205 H209 L212 E235 N239 E266
• 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	MN	A	D142 H205 T236 E238 E269	D139 H202 T233 E235 E266
BS02	MN	A	D131 D142 E269	D128 D139 E266
BS03	Y10	A	Y97 H114 D131 D142 T203 H205 F211 H212 E238 E269	Y94 H111 D128 D139 T200 H202 F208 H209 E235 E266	MOAD: ic50=0.76uM PDBbind-CN: -logKd/Ki=6.12,IC50=760nM

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