7A0F

The Crystal Structure of Bovine Thrombin in complex with Hirudin (C22U/C39U) at 2.7 Angstroms Resolution

• PDB DOI: https://doi.org/10.2210/pdb7A0F/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus, Hirudo medicinalis
• Mutation(s): Yes 


• Deposited: 2020-08-07 Released: 2021-03-17 
• Deposition Author(s): Hidmi, T., Mousa, R., Pomyalov, S., Lansky, S., Khouri, L., Metanis, N., Shoham, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.253 
• R-Value Work: 0.194 

Starting Model: experimental

Literature

Diselenide crosslinks for enhanced and simplified oxidative protein folding

Mousa, R., Hidmi, T., Pomyalov, S., Lansky, S., Khouri, L., Shalev, D.E., Shoham, G., Metanis, N.

(2021) Commun Chem 4: 30

• DOI: https://doi.org/10.1038/s42004-021-00463-9

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.82 kDa 
• Atom Count: 2,936 
• Modelled Residue Count: 359 
• Deposited Residue Count: 373 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	A [auth HHH]	259	Bos taurus	Mutation(s): 0  EC: 3.4.21.5
UniProt
Find proteins for P00735 (Bos taurus) Explore P00735  Go to UniProtKB:  P00735
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hirudin variant-1	B [auth III]	65	Hirudo medicinalis	Mutation(s): 2
UniProt
Find proteins for P01050 (Hirudo medicinalis) Explore P01050  Go to UniProtKB:  P01050

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	C [auth LLL]	49	Bos taurus	Mutation(s): 0  EC: 3.4.21.5
UniProt
Find proteins for P00735 (Bos taurus) Explore P00735  Go to UniProtKB:  P00735

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth HHH]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA	E [auth HHH]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.253 
• R-Value Work: 0.194 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.069	α = 90
b = 101.498	β = 90
c = 142.075	γ = 90

Software Package:

Software Name	Purpose
XDS	data processing
Aimless	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-17 
Deposition Author(s): Hidmi, T., Mousa, R., Pomyalov, S., Lansky, S., Khouri, L., Metanis, N., Shoham, G.

Revision History  

• Version 1.0: 2021-03-17
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Derived calculations, Refinement description