PDBsum entry 6t89

Hydrolase

PDB id: 6t89

Contents

Protein chains

28 a.a.

250 a.a.

11 a.a.

Ligands

MUQ

NAG

DMS

Metals

_NA ×2

Waters ×176

PDB id:

6t89

Name:

Hydrolase

Title:

Thrombin in complex with (s)-n-(tert-butyl)-4-(3-(3- carbamimidoylphenyl)-2-((2',4'-dimethoxy-[1,1'-biphenyl])-3- sulfonamido)propanoyl)piperazine-1-carboxamide (mi-498)

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. Tissue: blood. Synthetic: yes. Hirudo medicinalis. Medicinal leech. Organism_taxid: 6421

Resolution:

2.00Å R-factor: 0.174 R-free: 0.215

Authors:

S.A.Ngaha,A.Sandner,S.Huber,A.Heine,T.Steinmetzer,O.Pilgram

Key ref:

S.A.Ngaha et al. Thrombin in complex with (s)-N-(Tert-Butyl)-4-(3-(3-Carbamimidoylphenyl)-2-((2 4'-Dimethoxy-[1,1'-Biphenyl])-3-Sulfonamido)propanoyl piperazine-1-Carboxamide (mi-498). To be published, .

Date:

24-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: 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.