Structure of PDB 4bam Chain B

Receptor sequence

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

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQ

3D structure

• PDB: 4bam Identification of Structure-Kinetic and Structure-Thermodynamic Relationships for Thrombin Inhibitors.
• Chain: B
• Resolution: 1.88 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 I45 G46 M47 P49 W50 D149 H152 P153 C155 Y170 K171 R173 N194 M241 K242 N247 R248 W249	E8 I9 G10 M11 P13 W14 D113 H116 P117 C119 Y134 K135 R137 N157 M204 K205 N210 R211 W212
BS02	peptide	B	F55 L96 R98 R104 T105 R106 Y107 I114 M116	F19 L60 R62 R68 T69 R70 Y71 I78 M80
BS03	MM9	B	H79 Y83 W86 L132 I209 D229 A230 C231 S235 V255 W257 G258 G260 C261	H43 Y47 W50 L96 I172 D192 A193 C194 S198 V218 W220 G221 G223 C224	MOAD: Ki=1.14nM PDBbind-CN: -logKd/Ki=8.94,Ki=1.14nM

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