1DX5

Crystal structure of the thrombin-thrombomodulin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structural Basis for the Anticoagulant Activity of the Thrombin-Thrombomodulin Complex

Fuentes-Prior, P.Iwanaga, Y.Huber, R.Pagila, R.Rumennik, G.Seto, M.Morser, J.Light, D.R.Bode, W.

(2000) Nature 404: 518

  • DOI: 10.1038/35006683
  • Primary Citation of Related Structures:  
    1DX5

  • PubMed Abstract: 
  • The serine proteinase alpha-thrombin causes blood clotting through proteolytic cleavage of fibrinogen and protease-activated receptors and amplifies its own generation by activating the essential clotting factors V and VIII. Thrombomodulin, a transmembrane thrombin receptor with six contiguous epidermal growth factor-like domains (TME1-6), profoundly alters the substrate specificity of thrombin from pro- to anticoagulant by activating protein C ...

    The serine proteinase alpha-thrombin causes blood clotting through proteolytic cleavage of fibrinogen and protease-activated receptors and amplifies its own generation by activating the essential clotting factors V and VIII. Thrombomodulin, a transmembrane thrombin receptor with six contiguous epidermal growth factor-like domains (TME1-6), profoundly alters the substrate specificity of thrombin from pro- to anticoagulant by activating protein C. Activated protein C then deactivates the coagulation cascade by degrading activated factors V and VIII. The thrombin-thrombomodulin complex inhibits fibrinolysis by activating the procarboxypeptidase thrombin-activatable fibrinolysis inhibitor. Here we present the 2.3 A crystal structure of human alpha-thrombin bound to the smallest thrombomodulin fragment required for full protein-C co-factor activity, TME456. The Y-shaped thrombomodulin fragment binds to thrombin's anion-binding exosite-I, preventing binding of procoagulant substrates. Thrombomodulin binding does not seem to induce marked allosteric structural rearrangements at the thrombin active site. Rather, docking of a protein C model to thrombin-TME456 indicates that TME45 may bind substrates in such a manner that their zymogen-activation cleavage sites are presented optimally to the unaltered thrombin active site.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Martinsried, Germany. fuentes@biochem.mpg.de



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thrombin light chainA, B, C, D36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
PHAROS:  P00734
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ThrombomodulinE [auth I], F [auth J], G [auth K], H [auth L]118Homo sapiensMutation(s): 0 
Gene Names: THBDTHRM
UniProt & NIH Common Fund Data Resources
Find proteins for P07204 (Homo sapiens)
Explore P07204 
Go to UniProtKB:  P07204
PHAROS:  P07204
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Thrombin heavy chainI [auth M], J [auth N], K [auth O], L [auth P]259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
PHAROS:  P00734
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0GJ
Query on 0GJ

Download Ideal Coordinates CCD File 
AA [auth M] , BA [auth M] , CA [auth M] , DA [auth M] , GA [auth N] , HA [auth N] , IA [auth N] , JA [auth N] , 
AA [auth M],  BA [auth M],  CA [auth M],  DA [auth M],  GA [auth N],  HA [auth N],  IA [auth N],  JA [auth N],  MA [auth O],  NA [auth O],  OA [auth O],  PA [auth O],  TA [auth P],  UA [auth P],  VA [auth P],  WA [auth P]
L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide
C14 H28 Cl N6 O5
XELWNHKFCNMWQO-LPEHRKFASA-O
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
EA [auth N], KA [auth O], QA [auth P], Y [auth M]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
M [auth I], P [auth J], S [auth K], SA [auth P], V [auth L]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
N [auth I], Q [auth J], T [auth K], W [auth L]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
FA [auth N], LA [auth O], O [auth I], R [auth J], RA [auth P], U [auth K], X [auth L], Z [auth M]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 8
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000288 (0GJ)
Query on PRD_000288
AA [auth M] , BA [auth M] , CA [auth M] , DA [auth M] , GA [auth N] , HA [auth N] , IA [auth N] , JA [auth N] , 
AA [auth M],  BA [auth M],  CA [auth M],  DA [auth M],  GA [auth N],  HA [auth N],  IA [auth N],  JA [auth N],  MA [auth O],  NA [auth O],  OA [auth O],  PA [auth O],  TA [auth P],  UA [auth P],  VA [auth P],  WA [auth P]
GLU-GLY-ARG-CHLOROMETHYL KETONEPeptide-like /  Inhibitor  Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 214.4α = 90
b = 214.4β = 90
c = 131.41γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-04-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2016-12-21
    Changes: Advisory, Atomic model, Derived calculations, Non-polymer description, Other, Source and taxonomy
  • Version 2.0: 2018-06-27
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary