Structure of PDB 1ypk Chain H

Receptor sequence

>1ypkH (length=250) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF

3D structure

• PDB: 1ypk A Simple Protocol To Estimate Differences in Protein Binding Affinity for Enantiomers without Prior Resolution of Racemates
• Chain: H
• Resolution: 1.78 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 H119 P120 C122 Y134 K135 R137 N159 M201 K202 N205 R206 W207	E8 G10 M11 P13 W14 H116 P117 C119 Y134 K135 R137 N157 M204 K205 N210 R211 W212
BS02	peptide	H	F34 T74 R75 Y76 K81 I82	F19 T69 R70 Y71 K77 I78
BS03	CCR	H	H57 Y60A W60D E97A L99 D189 A190 S195 W215 G216 G219	H43 Y47 W50 E94 L96 D192 A193 S198 W220 G221 G223

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:1ypk, PDBe:1ypk, PDBj:1ypk
• PDBsum: 1ypk
• PubMed: 16374786
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)