Structure of PDB 1d3d Chain B

Receptor sequence

>1d3dB (length=250) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF

3D structure

• PDB: 1d3d The crystal structures of human alpha-thrombin complexed with active site-directed diamino benzo[b]thiophene derivatives: a binding mode for a structurally novel class of inhibitors
• Chain: B
• Resolution: 2.04 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H79 D135 E238 G239 D240 S241 G242
• 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 M47 P49 W50 D149 H152 P153 C155 Y170 K171 R173 N200 M247 K248 R254 W255	E8 M11 P13 W14 D113 H116 P117 C119 Y134 K135 R137 N157 M204 K205 R211 W212
BS02	peptide	B	F55 L96 R104 T105 R106 Y107 K113 I114	F19 L60 R68 T69 R70 Y71 K77 I78
BS03	BZT	B	H79 Y83 W86 L132 D235 A236 C237 E238 V261 S262 W263 G264	H43 Y47 W50 L96 D192 A193 C194 E195 V218 S219 W220 G221	MOAD: Ka=1240000000M^-1 PDBbind-CN: -logKd/Ki=9.09,Kd=0.81nM BindingDB: Ki=2.1nM

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:1d3d, PDBe:1d3d, PDBj:1d3d
• PDBsum: 1d3d
• PubMed: 10739244
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)