Structure of PDB 4ud9 Chain H

Receptor sequence

>4ud9H (length=254) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTA
GQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGD
SGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVI
DQFG

3D structure

• PDB: 4ud9 Fragments Can Bind Either More Enthalpy or Entropy-Driven: Crystal Structures and Residual Hydration Pattern Suggest Why.
• Chain: H
• Resolution: 1.124 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	F34 L40 L65 R67 R73 T74 R75 Y76 K81 I82 G246	F19 L26 L60 R62 R68 T69 R70 Y71 K77 I78 G254
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 N160 M207 K208 N213 R214 W215
BS03	FQI	H	D189 A190 C191 E192 V213 W215 G216 G219 G226 F227	D195 A196 C197 E198 V221 W223 G224 G226 G234 F235	MOAD: Kd=475uM BindingDB: Kd=507000nM,Ki=431000nM

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:4ud9, PDBe:4ud9, PDBj:4ud9
• PDBsum: 4ud9
• PubMed: 26270568
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)