Structure of PDB 3dhk Chain H

Receptor sequence

>3dhkH (length=250) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKEGQPS
VLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGP
FVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG

3D structure

• PDB: 3dhk Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin
• Chain: H
• Resolution: 1.73 Å

Enzymatic activity

• Enzyme Commision number: 3.4.21.5: thrombin.

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	peptide	H	E23 G25 M26 P28 W29 D116 H119 P120 C122 Y134 K135 R137 N159 M201 K202 R206 W207	E8 G10 M11 P13 W14 D113 H116 P117 C119 Y134 K135 R137 N156 M203 K204 R210 W211
BS02	peptide	H	F34 Q38 L40 L65 R73 T74 R75 Y76 I82	F19 Q24 L26 L60 R68 T69 R70 Y71 I78
BS03	23U	H	Y60A W60D A190 C191 S195 V213 S214 W215 G216 E217 F227	Y47 W50 A192 C193 S197 V217 S218 W219 G220 E221 F231	MOAD: Ki=47nM PDBbind-CN: -logKd/Ki=7.33,Ki=47nM BindingDB: IC50=12nM

Gene Ontology

Molecular Function

• GO:0004252 serine-type endopeptidase activity
• GO:0005509 calcium ion binding

Biological Process

• GO:0006508 proteolysis
• GO:0007596 blood coagulation

External links

• PDB: RCSB:3dhk, PDBe:3dhk, PDBj:3dhk
• PDBsum: 3dhk
• PubMed: 19520086
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)