Structure of PDB 2gde Chain H

Receptor sequence

>2gdeH (length=249) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQ

3D structure

• PDB: 2gde Total synthesis and structural confirmation of chlorodysinosin A.
• Chain: H
• Resolution: 2.0 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 G136 R137 N159 K202 P204 N205 R206 W207	E8 I9 G10 M11 P13 W14 D113 H116 P117 C119 Y134 K135 G136 R137 N157 K205 P207 N210 R211 W212
BS02	peptide	H	K36 Q38 E39 L40 L65 R67 R73 T74 R75 Y76 I82	K21 Q24 E25 L26 L60 R62 R68 T69 R70 Y71 I78
BS03	SN3	H	Y60A W60D I174 D189 A190 C191 S195 W215 G216 E217 G219 R221A	Y47 W50 I172 D192 A193 C194 S198 W220 G221 E222 G223 R226	MOAD: ic50=5.7nM PDBbind-CN: -logKd/Ki=8.24,IC50=5.7nM

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:2gde, PDBe:2gde, PDBj:2gde
• PDBsum: 2gde
• PubMed: 16895415
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)