Structure of PDB 1yvm Chain A

Receptor sequence

>1yvmA (length=262) Species: 562 (Escherichia coli)

AISIKTPEDIEKMRVAGRLAAEVLEMIEPYVKPGVSTGELDRICNDYIVN
EQHAVSACLGYHGYPKSVCISINEVVCHGIPDDAKLLKDGDIVNIDVTVI
KDGFHGDTSKMFIVGKPTIMGERLCRITQESLYLALRMVKPGINLREIGA
AIQKFVEAEGFSVVREYCGHGIGQGFHEEPQVLHYDSRETNVVLKPGMTF
TIEPMVNAGKKEIRTMKDGWTVKTKDRSLSAQYEHTIVVTDNGCEILTLR
KDDTIPAIISHD

3D structure

• PDB: 1yvm Metal Ions as Cofactors for the Binding of Inhibitors to Methionine Aminopeptidase: A Critical View of the Relevance of In Vitro Metalloenzyme Assays.
• Chain: A
• Resolution: 1.6 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H79 D97 D108 H171 Q175 H178 Q182 E204 N208 Q233 E235
• Catalytic site (residue number reindexed from 1): H78 D96 D107 H170 Q174 H177 Q181 E203 N207 Q232 E234
• 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	CO	A	D97 D108 E235	D96 D107 E234
BS02	CO	A	D108 H171 T202 E204 E235	D107 H170 T201 E203 E234
BS03	TMG	A	C59 Y62 Y65 C70 H79 H178	C58 Y61 Y64 C69 H78 H177	MOAD: Ki=0.4uM PDBbind-CN: -logKd/Ki=6.40,Ki=0.4uM BindingDB: IC50=472nM

Gene Ontology

Molecular Function

• GO:0004177 aminopeptidase activity
• GO:0004239 initiator methionyl aminopeptidase activity
• GO:0008198 ferrous iron binding
• GO:0008235 metalloexopeptidase activity
• GO:0046872 metal ion binding
• GO:0046914 transition metal ion binding
• GO:0070006 metalloaminopeptidase activity

Biological Process

• GO:0006508 proteolysis

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:1yvm, PDBe:1yvm, PDBj:1yvm
• PDBsum: 1yvm
• PubMed: 15880695
• UniProt: P0AE18|MAP1_ECOLI Methionine aminopeptidase (Gene Name=map)