Structure of PDB 1ypj Chain H

Receptor sequence

>1ypjH (length=251) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWGQ
PSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSG
GPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQ
F

3D structure

• PDB: 1ypj 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 I24 G25 M26 P28 W29 D116 H119 P120 C122 Y134 K135 R137 N159 M201 K202 N205 R206 W207	E8 I9 G10 M11 P13 W14 D113 H116 P117 C119 Y134 K135 R137 N158 M205 K206 N211 R212 W213
BS02	peptide	H	F34 K36 Q38 R67 R73 T74 R75 Y76 K81 I82	F19 K21 Q24 R62 R68 T69 R70 Y71 K77 I78
BS03	UIB	H	H57 Y60A W60D E97A N98 L99 D189 A190 E192 S195 S214 W215 G216 G219	H43 Y47 W50 E94 N95 L96 D193 A194 E196 S199 S220 W221 G222 G224	MOAD: Ki=95nM PDBbind-CN: -logKd/Ki=7.02,Ki=95nM

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