Structure of PDB 1ypm Chain H

Receptor sequence

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

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF

3D structure

• PDB: 1ypm Design and X-ray crystal structures of human thrombin with synthetic cyanopeptide-analogues.
• Chain: H
• Resolution: 1.85 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 N157 M204 K205 N210 R211 W212
BS02	peptide	H	F34 L65 R67 R73 T74 Y76 I82	F19 L60 R62 R68 T69 Y71 I78
BS03	RA4	H	H57 Y60A W60D N98 D189 A190 S195 S214 W215 G216 E217 G219 R221A	H43 Y47 W50 N95 D192 A193 S198 S219 W220 G221 E222 G223 R226	MOAD: Ki=1.9uM

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:1ypm, PDBe:1ypm, PDBj:1ypm
• PDBsum: 1ypm
• PubMed: 17341023
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)