PDBsum entry 6y9h

Hydrolase

PDB id: 6y9h

Contents

Protein chains

28 a.a.

250 a.a.

11 a.a.

Ligands

DPN-PRO-OGZ

DMS

PO4 ×2

NAG

Metals

_NA ×2

Waters ×266

PDB id:

6y9h

Name:

Hydrolase

Title:

Thrombin in complex with d-phe-pro-m-trifluoromethylbenzylamide derivative (phe2)

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. Synthetic construct. Organism_taxid: 32630

Resolution:

1.48Å R-factor: 0.139 R-free: 0.170

Authors:

A.Sandner,A.Heine,G.Klebe,N.Abazi

Key ref:

A.Sandner et al. Thrombin in complex with d-Phe-Pro-M-Trifluoromethylbenzylamide derivative (ph. To be published, .

Date:

09-Mar-20 Release date: 31-Mar-21

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: 250 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.