Structure of PDB 1y3g Chain E

Receptor sequence

>1y3gE (length=316) Species: 1427 (Bacillus thermoproteolyticus)

ITGTSTVGVGRGVLGDQKNINTTYSTYYYLQDNTRGNGIFTYDAKYRTTL
PGSLWADADNQFFASYDAPAVDAHYYAGVTYDYYKNVHNRLSYDGNNAAI
RSSVHYSQGYNNAFWNGSQMVYGDGDGQTFIPLSGGIDVVAHELTHAVTD
YTAGLIYQNESGAINEAISDIFGTLVEFYANKNPDWEIGEDVYTPGISGD
SLRSMSDPAKYGDPDHYSKRYTGTQDNGGVHINSGIINKAAYLISQGGTH
YGVSVVGIGRDKLGKIFYRALTQYLTPTSNFSQLRAAAVQSATDLYGSTS
QEVASVKQAFDAVGVK

3D structure

• PDB: 1y3g Structural Analysis of Silanediols as Transition-State-Analogue Inhibitors of the Benchmark Metalloprotease Thermolysin(,).
• Chain: E
• Resolution: 2.1 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H142 E143 H146 Y157 E166 D226 H231
• Catalytic site (residue number reindexed from 1): H142 E143 H146 Y157 E166 D226 H231
• Enzyme Commision number: 3.4.24.27: thermolysin.

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	CA	E	D138 E177 D185 E187 E190	D138 E177 D185 E187 E190
BS02	CA	E	E177 N183 D185 E190	E177 N183 D185 E190
BS03	CA	E	D57 D59 Q61	D57 D59 Q61
BS04	CA	E	Y193 T194 I197 D200	Y193 T194 I197 D200
BS05	ZN	E	H142 H146 E166	H142 H146 E166
BS06	AMM	E	A113 E143 H146 E166 L202 R203 H231	A113 E143 H146 E166 L202 R203 H231	PDBbind-CN: -logKd/Ki=7.40,Ki=40nM
BS07	LEU	E	N112 H231	N112 H231	PDBbind-CN: -logKd/Ki=7.40,Ki=40nM

Gene Ontology

Molecular Function

• GO:0004222 metalloendopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:1y3g, PDBe:1y3g, PDBj:1y3g
• PDBsum: 1y3g
• PubMed: 16342943
• UniProt: P00800|THER_BACTH Thermolysin (Gene Name=npr)