Structure of PDB 2vkm Chain A

Receptor sequence
>2vkmA (length=389) Species: 9606 (Homo sapiens) [Search protein sequence]
GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHP
FLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVR
ANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHV
PNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRRE
WYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVK
SIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSF
RITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFD
RARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN
3D structure
PDB2vkm Potent Memapsin 2 (Beta-Secretase) Inhibitors: Design, Synthesis, Protein-Ligand X-Ray Structure, and in Vivo Evaluation.
ChainA
Resolution2.05 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) D32 S35 N37 A39 Y71 D228 T231
Catalytic site (residue number reindexed from 1) D36 S39 N41 A43 Y75 D232 T235
Enzyme Commision number 3.4.23.46: memapsin 2.
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 BSD A Q12 G13 L30 D32 G34 S35 Y71 T72 Q73 F108 W115 I118 D228 G230 T231 T232 N233 R235 Q16 G17 L34 D36 G38 S39 Y75 T76 Q77 F112 W119 I122 D232 G234 T235 T236 N237 R239 MOAD: Ki=1.8nM
PDBbind-CN: -logKd/Ki=8.74,Ki=1.8nM
BindingDB: IC50=1nM,Ki=1.8nM
Gene Ontology
Molecular Function
GO:0004190 aspartic-type endopeptidase activity
Biological Process
GO:0006508 proteolysis
Cellular Component
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2vkm, PDBe:2vkm, PDBj:2vkm
PDBsum2vkm
PubMed18180160
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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