Structure of PDB 4dii Chain H

Receptor sequence

>4diiH (length=250) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETQPS
VLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGP
FVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG

3D structure

• PDB: 4dii High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity.
• Chain: H
• Resolution: 2.05 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 W29 D116 H119 P120 C122 Y134 K135 R137 N159 K202 N205 R206 W207	E8 G10 M11 W14 D113 H116 P117 C119 Y134 K135 R137 N156 K204 N209 R210 W211
BS02	dna	H	H71 R75 Y76 R77A N78 I79 Y117	H66 R70 Y71 R73 N74 I75 Y114
BS03	0G6	H	H57 Y60A W60D L99 D189 A190 S195 W215 G216	H43 Y47 W50 L96 D191 A192 S197 W219 G220

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:4dii, PDBe:4dii, PDBj:4dii
• PDBsum: 4dii
• PubMed: 22669903
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)