Structure of PDB 4yes Chain B

Receptor sequence

>4yesB (length=252) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF
GE

3D structure

• PDB: 4yes Improved Stability of Proline-Derived Direct Thrombin Inhibitors through Hydroxyl to Heterocycle Replacement.
• Chain: B
• Resolution: 1.5 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H406 D462 E565 G566 D567 S568 G569
• 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	B	E371 G373 M374 P376 W377 F474 D476 H479 P480 C482 Y497 K498 R500 N527 M574 K575 N580 R581 W582	E8 G10 M11 P13 W14 F111 D113 H116 P117 C119 Y134 K135 R137 N157 M204 K205 N210 R211 W212
BS02	peptide	B	F382 Q387 L389 L423 R431 T432 Y434 I441	F19 Q24 L26 L60 R68 T69 Y71 I78
BS03	MG	B	R596 K599	R226 K229
BS04	45S	B	H406 W413 A563 C564 S568 V588 S589 W590 G591 G593 G601 F602	H43 W50 A193 C194 S198 V218 S219 W220 G221 G223 G231 F232	MOAD: Ki=9.6nM PDBbind-CN: -logKd/Ki=8.02,Ki=9.6nM

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:4yes, PDBe:4yes, PDBj:4yes
• PDBsum: 4yes
• PubMed: 26005532
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)