Structure of PDB 4ufd Chain H

Receptor sequence

>4ufdH (length=251) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF
G

3D structure

• PDB: 4ufd Boosting Affinity by Correct Ligand Preorganization for the S2 Pocket of Thrombin: A Study by Isothermal Titration Calorimetry, Molecular Dynamics, and High-Resolution Crystal Structures.
• Chain: H
• Resolution: 1.429 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	L65 Y76 K81 I82	L60 Y71 K77 I78
BS02	peptide	H	E23 G25 M26 P28 W29 D116 H119 P120 C122 Y134 K135 R137 N159 M201 K202 N205 R206 W207	E8 G10 M11 P13 W14 D113 H116 P117 C119 Y134 K135 R137 N157 M204 K205 N210 R211 W212
BS03	S49	H	H57 Y60A W60D N98 L99 D189 A190 E192 V213 S214 W215 G216 G219 C220	H43 Y47 W50 N95 L96 D192 A193 E195 V218 S219 W220 G221 G223 C224	PDBbind-CN: -logKd/Ki=9.68,Ki=0.21nM

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:4ufd, PDBe:4ufd, PDBj:4ufd
• PDBsum: 4ufd
• PubMed: 26762840
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)