Structure of PDB 2zda Chain H

Receptor sequence

>2zdaH (length=251) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF
G

3D structure

• PDB: 2zda 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 I47 S48 F114 D116 H119 P120 C122 Y134 K135 R137 N159 M201 K202 N205 R206 W207	E8 G10 M11 P13 W14 I33 S34 F111 D113 H116 P117 C119 Y134 K135 R137 N157 M204 K205 N210 R211 W212
BS02	peptide	H	F34 L40 L65 R73 T74 Y76 K81 I82	F19 L26 L60 R68 T69 Y71 K77 I78
BS03	32U	H	Y60A L99 I174 D189 A190 V213 W215 G216	Y47 L96 I172 D192 A193 V218 W220 G221	PDBbind-CN: -logKd/Ki=8.40,Ki=4nM

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:2zda, PDBe:2zda, PDBj:2zda
• PDBsum: 2zda
• PubMed: 19520086
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)