Structure of PDB 3qdz Chain D

Receptor sequence

>3qdzD (length=257) Species: 9606 (Homo sapiens)

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRNI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTA
NVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDA
CEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWI
QKVIDQF

3D structure

• PDB: 3qdz Molecular dissection of Na+ binding to thrombin.
• Chain: D
• Resolution: 2.8 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H57 N102 E192 G193 D194 S195 G196
• Catalytic site (residue number reindexed from 1): H43 N99 E202 G203 D204 S205 G206
• 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	D	E23 M26 S115 H119 P120 V121 C122 L129C Y134 K135 R137 N159 M201 K202 N205 R206 W207	E8 M11 S112 H116 P117 V118 C119 L129 Y134 K135 R137 N164 M211 K212 N217 R218 W219
BS02	peptide	D	H57 W60D I174 D189 A190 E192 G193 S195 G216	H43 W50 I179 D199 A200 E202 G203 S205 G228

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:3qdz, PDBe:3qdz, PDBj:3qdz
• PDBsum: 3qdz
• UniProt: P00734|THRB_HUMAN Prothrombin (Gene Name=F2)