Structure of PDB 3p70 Chain D

Receptor sequence

>3p70D (length=250) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKEKGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF

3D structure

• PDB: 3p70 Structural basis of thrombin-mediated factor V activation: the Glu666-Glu672 sequence is critical for processing at the heavy chain-B domain junction.
• Chain: D
• Resolution: 2.55 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	D	E371 M374 P376 W377 H479 P480 V481 C482 Y497 K498 R500 N527 M574 K575 R581 W582	E8 M11 P13 W14 H116 P117 V118 C119 Y134 K135 R137 N157 M204 K205 R211 W212
BS02	peptide	D	F382 R431 T432 R433 Y434	F19 R68 T69 R70 Y71
BS03	BEN	D	D562 A563 S568 V588 W590 G591	D192 A193 S198 V218 W220 G221

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:3p70, PDBe:3p70, PDBj:3p70
• PDBsum: 3p70
• PubMed: 21555742
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)