Structure of PDB 6zv8 Chain H

Receptor sequence

>6zv8H (length=250) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF

3D structure

• PDB: 6zv8 Design, Synthesis, and Pharmacological Characterization of a Neutral, Non-Prodrug Thrombin Inhibitor with Good Oral Pharmacokinetics.
• Chain: H
• Resolution: 1.7 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H57 D102 E192 G193 D194 S195 G196
• Catalytic site (residue number reindexed from 1): H43 D99 E195 G196 D197 S198 G199
• 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 R75 Y76 I82	F19 L60 R62 R68 T69 R70 Y71 I78
BS03	QQT	H	H57 Y60A W60D N98 L99 I174 D189 A190 C191 E192 S195 V213 S214 W215 G216 G219 G226 F227	H43 Y47 W50 N95 L96 I172 D192 A193 C194 E195 S198 V218 S219 W220 G221 G223 G231 F232	MOAD: ic50=0.7nM BindingDB: IC50=1.20nM

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:6zv8, PDBe:6zv8, PDBj:6zv8
• PDBsum: 6zv8
• PubMed: 33108181
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)