Structure of PDB 4bak Chain B

Receptor sequence

>4bakB (length=249) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQ

3D structure

• PDB: 4bak Identification of Structure-Kinetic and Structure-Thermodynamic Relationships for Thrombin Inhibitors.
• Chain: B
• Resolution: 1.94 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H79 D135 E232 G233 D234 S235 G236
• 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	E44 G46 M47 P49 W50 D149 H152 P153 C155 Y170 K171 R173 N194 M241 K242 N247 R248 W249	E8 G10 M11 P13 W14 D113 H116 P117 C119 Y134 K135 R137 N157 M204 K205 N210 R211 W212
BS02	peptide	B	F55 Q60 L96 R98 R104 T105 R106 Y107 K113 I114	F19 Q24 L60 R62 R68 T69 R70 Y71 K77 I78
BS03	M67	B	H79 Y83 W86 I209 D229 A230 E232 S235 W257 G258 E259 G260 C261	H43 Y47 W50 I172 D192 A193 E195 S198 W220 G221 E222 G223 C224	MOAD: Ki=1.22nM PDBbind-CN: -logKd/Ki=8.91,Ki=1.22nM

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:4bak, PDBe:4bak, PDBj:4bak
• PDBsum: 4bak
• PubMed: 23290007
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)