Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.30 kDa 
• Atom Count: 2722 
• Residue Count: 297 
• Unique protein chains: 4

3VXE

Human alpha-thrombin-Bivalirudin complex at PD5.0

• DOI: 10.2210/pdb3VXE/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2012-09-12 Released: 2013-09-04 
• Deposition Author(s): Yamada, T., Kurihara, K., Masumi, K., Tamada, T., Tomoyori, K., Ohnishi, Y., Tanaka, I., Kuroki, R., Niimura, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.178 
• R-Value Observed: 0.144 

Literature

Neutron and X-ray crystallographic analysis of the human alpha-thrombin-bivalirudin complex at pD 5.0: protonation states and hydration structure of the enzyme-product complex

Yamada, T., Kurihara, K., Ohnishi, Y., Tamada, T., Tomoyori, K., Masumi, K., Tanaka, I., Kuroki, R., Niimura, N.

(2013) Biochim Biophys Acta 1834: 1532-1538

• PubMed: 23712263 
• DOI: 10.1016/j.bbapap.2013.05.014
• Primary Citation of Related Structures:  
  3VXE, 3VXF


• PubMed Abstract: 
  

The protonation states and hydration structures of the α-thrombin-bivalirudin complex were studied by joint XN refinement of the single crystal X-ray and neutron diffraction data at resolutions of 1.6 and 2.8Å, respectively. The atomic distances were estimated by carrying out X-ray crystallographic analysis at 1.25Å resolution. The complex represents a model of the enzyme-product (EP) complex of α-thrombin. The neutron scattering length maps around the active site suggest that the side chain of H57/H was deuterated. The joint XN refinement showed that occupancies for Dδ1 and Dε2 of H57/H were 1.0 and 0.7, respectively. However, no significant neutron scattering length density was observed around the hydroxyl oxygen Oγ of S195/H, which was close to the carboxylic carbon atom of dFPR-COOH. These observations suggest that the Oγ atom of S195/H is deprotonated and maintains its nucleophilicity in the EP complex. In addition to the active site, the hydration structures of the S1 subsite and the Exosite I, which are involved in the recognition of bivalirudin, are presented.

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Organizational Affiliation: 

Ibaraki University, Tokai, Ibaraki, Japan. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin light chain	L	36	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin heavy chain	H	259	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
BIVALIRUDIN	J	17	N/A	Mutation(s): 0
Find proteins for P28504 (Hirudo medicinalis) Explore P28504  Go to UniProtKB:  P28504

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
BIVALIRUDIN	I	3	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	H	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001145	J	BIVALIRUDIN N-terminus fragment	Peptide-like /  Thrombin inhibitor		--

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001148	I	BIVALIRUDIN C-terminus fragment	Peptide-like /  Thrombin inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.178 
• R-Value Observed: 0.144 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.787	α = 90
b = 106.618	β = 90
c = 45.574	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-09-12 
• Released Date: 2013-09-04 
Deposition Author(s): Yamada, T., Kurihara, K., Masumi, K., Tamada, T., Tomoyori, K., Ohnishi, Y., Tanaka, I., Kuroki, R., Niimura, N.

Revision History 

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary