Structure of PDB 6yb6 Chain H

Receptor sequence

>6yb6H (length=250) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF

3D structure

• PDB: 6yb6 Thrombin in complex with D-Phe-Pro-3-chloro-1,3-dihydroxybenzylamide derivative (13c)
• Chain: H
• Resolution: 1.33 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 G25 M26 P28 W29 D116 H119 P120 C122 Y134 K135 R137 N159 M201 K202 P204 N205 R206 W207	E8 G10 M11 P13 W14 D113 H116 P117 C119 Y134 K135 R137 N157 M204 K205 P207 N210 R211 W212
BS02	peptide	H	F34 L40 L65 R73 T74 R75 Y76 K81 I82	F19 L26 L60 R68 T69 R70 Y71 K77 I78
BS03	peptide	H	E97A N98 I174 W215 G216	E94 N95 I172 W220 G221
BS04	PRO	H	H57 Y60A W60D L99	H43 Y47 W50 L96
BS05	OJK	H	H57 S195 S214 W215 G216 G219 C220	H43 S198 S219 W220 G221 G223 C224

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:6yb6, PDBe:6yb6, PDBj:6yb6
• PDBsum: 6yb6
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)