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PDBsum entry 6yb6
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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
6yb6

 

 

 

 

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Contents
Protein chains
28 a.a.
250 a.a.
11 a.a.
Ligands
DPN-PRO-OJK
DMS ×2
NAG
PO4
Metals
_NA ×2
Waters ×251
PDB id:
6yb6
Name: Hydrolase
Title: Thrombin in complex with d-phe-pro-3-chloro-1,3-dihydroxybenzylamide derivative (13c)
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:
1.33Å     R-factor:   0.132     R-free:   0.153
Authors: A.Sandner,A.Heine,G.Klebe,N.Abazi
Key ref: A.Sandner et al. Thrombin in complex with d-Phe-Pro-3-Chloro-1,3-Dihydroxybenzylamide derivativ. To be published, .
Date:
16-Mar-20     Release date:   31-Mar-21    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		622 a.a.
28 a.a.
Protein chain
Pfam   ArchSchema ?
P00734  (THRB_HUMAN) -  Prothrombin from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		622 a.a.
250 a.a.
Protein chain
Pfam   ArchSchema ?
P09945  (HIRV2_HIRME) -  Hirudin variant-2 (Fragment) from Hirudo medicinalis
Seq:
Struc: 		72 a.a.
11 a.a.*
Key:    PfamA domain  Secondary structure
* 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.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Arg-|-Gly; activates fibrinogen to fibrin and releases fibrinopeptide A and B.

 

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