Structure of PDB 3b23 Chain B

Receptor sequence

>3b23B (length=259) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTA
NVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDA
CEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWI
QKVIDQFGE

3D structure

• PDB: 3b23 Crystal structure of thrombin in complex with s-variegin: insights of a novel mechanism of inhibition and design of tunable thrombin inhibitors
• Chain: B
• Resolution: 2.4 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 E202 G203 D204 S205 G206
• 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	E23 I24 G25 M26 W29 D116 H119 P120 C122 G133 Y134 K135 R137 N159 M201 K202 N205 R206 W207	E8 I9 G10 M11 W14 D113 H116 P117 C119 G133 Y134 K135 R137 N164 M211 K212 N217 R218 W219
BS02	peptide	B	F34 E39 L40 L41 K60F R67 R73 T74 R75 Y76 R77A Q151 E192	F19 E25 L26 L27 K52 R62 R68 T69 R70 Y71 R73 Q156 E202

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:3b23, PDBe:3b23, PDBj:3b23
• PDBsum: 3b23
• PubMed: 22053189
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)