PDBsum entry 6t52

Hydrolase

PDB id: 6t52

Contents

Protein chains

28 a.a.

251 a.a.

11 a.a.

Ligands

PO4

DMS

MJH

NAG

Metals

_NA ×2

Waters ×216

PDB id:

6t52

Name:

Hydrolase

Title:

Thrombin in complex with a d-phe-pro-imidazole derivative

Structure:

Prothrombin. Chain: l. Synonym: coagulation factor ii. Prothrombin. Chain: h. Synonym: coagulation factor ii. Hirudin variant-2. Chain: i. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Synthetic: yes. Hirudo medicinalis. Medicinal leech. Organism_taxid: 6421

Resolution:

1.45Å R-factor: 0.131 R-free: 0.161

Authors:

K.Ngo,N.Abazi,A.Heine,G.Klebe

Date:

15-Oct-19 Release date: 18-Nov-20

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 28 a.a.

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 251 a.a.

Protein chain

P09945  (HIRV2_HIRME) -  Hirudin variant-2 (Fragment) from Hirudo medicinalis

Seq: 72 a.a.

Struc: 11 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains L, H: E.C.3.4.21.5 - thrombin.
• Reaction: Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.