PDBsum entry 2bvr

Hydrolase/hydrolase inhibitor

PDB id: 2bvr

Contents

Protein chains

251 a.a. *

11 a.a. *

28 a.a. *

Ligands

4CP

Waters ×454

* Residue conservation analysis

PDB id:

2bvr

Name:

Hydrolase/hydrolase inhibitor

Title:

Human thrombin complexed with fragment-based small molecules occupying the s1 pocket

Structure:

Alpha thrombin. Chain: h. Fragment: large subunit, residues 364-622. Synonym: coagulation factor ii. Engineered: yes. Hirudin variant-2. Chain: i. Engineered: yes. Alpha thrombin.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Hirudo medicinalis. Medicinal leech. Organism_taxid: 6421.

Biol. unit:

Trimer (from PDB file)

Resolution:

1.25Å R-factor: 0.210 R-free: 0.229

Authors:

T.Neumann,H.-D.Junker,O.Keil,K.Burkert,H.Ottleben,J.Gamer,R.Sekul, H.Deppe,A.Feurer,D.Tomandl,G.Metz

Key ref:

T.Neumann et al. (2005). Discovery of thrombin inhibitor fragments from chemical microarray screening. Lett drug des discovery, 2, 590.

Date:

04-Jul-05 Release date: 25-Oct-06

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.*

Protein chain

P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens

Seq: 622 a.a.

Struc: 28 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

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