Structure of PDB 1d3q Chain B

Receptor sequence

>1d3qB (length=250) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF

3D structure

• PDB: 1d3q 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: 2.9 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 G46 M47 P49 W50 H152 P153 C155 Y170 K171 R173 N200 M247 K248 R254 W255	E8 G10 M11 P13 W14 H116 P117 C119 Y134 K135 R137 N157 M204 K205 R211 W212
BS02	peptide	B	F55 Q60 L96 R104 T105 R106 Y107 K113 I114	F19 Q24 L60 R68 T69 R70 Y71 K77 I78
BS03	BT2	B	Y83 W86 E130 N131 L132 I215 A236 C237 E238 S262 W263 G264 C267	Y47 W50 E94 N95 L96 I172 A193 C194 E195 S219 W220 G221 C224	PDBbind-CN: -logKd/Ki=6.54,Kd=0.29uM

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:1d3q, PDBe:1d3q, PDBj:1d3q
• PDBsum: 1d3q
• PubMed: 10739244
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)