Structure of PDB 1bb0 Chain B

Receptor sequence

>1bb0B (length=249) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKPQELLCGASLISDRWVLTAAHCLLYPPWD
KNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIA
LMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKEGQPSV
LQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPF
VMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG

3D structure

• PDB: 1bb0 Highly selective mechanism-based thrombin inhibitors: structures of thrombin and trypsin inhibited with rigid peptidyl aldehydes.
• Chain: B
• Resolution: 2.1 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H57 D102 E192 G193 D194 S195 G196
• Catalytic site (residue number reindexed from 1): H42 D98 E193 G194 D195 S196 G197
• 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 P28 W29 D116 H119 P120 C122 Y134 K135 R137 N159 M201 K202 R206 W207	E8 I9 G10 M11 P13 W14 D112 H115 P116 C118 Y133 K134 R136 N155 M202 K203 R209 W210
BS02	peptide	B	F34 R67 R73 T74 R75 Y76 K81 I82	F19 R61 R67 T68 R69 Y70 K76 I77
BS03	0IV	B	H57 Y60A W60D I174 D189 C191 S195 S214 W215 G216 G219	H42 Y46 W49 I170 D190 C192 S196 S217 W218 G219 G221	PDBbind-CN: -logKd/Ki=8.36,Ki=4.4nM BindingDB: IC50=28.8nM

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:1bb0, PDBe:1bb0, PDBj:1bb0
• PDBsum: 1bb0
• PubMed: 9724521
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)