RCSB PDB - 1DX5: Crystal structure of the thrombin-thrombomodulin complex (original) (raw)
Crystal structure of the thrombin-thrombomodulin complex
This is version 2.3 of the entry. See complete history.
Structural Basis for the Anticoagulant Activity of the Thrombin-Thrombomodulin Complex
[Fuentes-Prior, P.](/search?q=citation.rcsb%5Fauthors:Fuentes-Prior, P.), [Iwanaga, Y.](/search?q=citation.rcsb%5Fauthors:Iwanaga, Y.), [Huber, R.](/search?q=citation.rcsb%5Fauthors:Huber, R.), [Pagila, R.](/search?q=citation.rcsb%5Fauthors:Pagila, R.), [Rumennik, G.](/search?q=citation.rcsb%5Fauthors:Rumennik, G.), [Seto, M.](/search?q=citation.rcsb%5Fauthors:Seto, M.), [Morser, J.](/search?q=citation.rcsb%5Fauthors:Morser, J.), [Light, D.R.](/search?q=citation.rcsb%5Fauthors:Light, D.R.), [Bode, W.](/search?q=citation.rcsb%5Fauthors:Bode, W.)
(2000) Nature 404: 518
PubMed: 10761923 Search on PubMed
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. 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
Macromolecule Content
- Total Structure Weight: 194.11 kDa
- Atom Count: 14,018
- Modelled Residue Count: 1,652
- Deposited Residue Count: 1,652
- Unique protein chains: 3
Find similar proteins by:
(by identity cutoff) | 3D Structure
Find similar proteins by:
(by identity cutoff) | 3D Structure
Find similar proteins by:
(by identity cutoff) | 3D Structure
| Ligands 5 Unique | ||||
|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions |
| 0GJQuery on 0GJDownload Ideal Coordinates CCD File | AA [auth M]BA [auth M]CA [auth M]DA [auth M]GA [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}glycinamideC14 H28 Cl N6 O5XELWNHKFCNMWQO-LPEHRKFASA-O |  |
Interactions |
| NAGQuery on NAGDownload Ideal Coordinates CCD File | EA [auth N],KA [auth O],QA [auth P],Y [auth M] | 2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O6OVRNDRQMDRJTHS-FMDGEEDCSA-N |  |
Interactions |
| FMTQuery on FMTDownload Ideal Coordinates CCD File | M [auth I],P [auth J],S [auth K],SA [auth P],V [auth L] | FORMIC ACIDC H2 O2BDAGIHXWWSANSR-UHFFFAOYSA-N |  |
Interactions |
| CAQuery on CADownload Ideal Coordinates CCD File | N [auth I],Q [auth J],T [auth K],W [auth L] | CALCIUM IONCaBHPQYMZQTOCNFJ-UHFFFAOYSA-N |  |
Interactions |
| NAQuery on NADownload Ideal Coordinates CCD File | FA [auth N]LA [auth O]O [auth I]R [auth J]RA [auth P]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 IONNaFKNQFGJONOIPTF-UHFFFAOYSA-N |  |
Interactions |
Biologically Interesting Molecules (External Reference) 1 Unique
| Entity ID: 8 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_000288 (0GJ)Query on PRD_000288 | AA [auth M]BA [auth M]CA [auth M]DA [auth M]GA [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 KETONE](/search?q=pdbx%5Freference%5Fmolecule.name:=GLU-GLY-ARG-CHLOROMETHYL KETONE) | Peptide-like / Inhibitor | |
Interactions |
Experimental Data & Validation
Experimental Data
- Space Group: [H 3](/search?q=symmetry.space%5Fgroup%5Fname%5FH%5FM:H 3)
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 214.4 | α = 90 |
| b = 214.4 | β = 90 |
| c = 131.41 | γ = 120 |
Software Package:
| Software Name | Purpose |
|---|---|
| X-PLOR | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| X-PLOR | phasing |
Deposition Data
- Released Date: 2000-04-10 Deposition Author(s): [Fuentes-Prior, P.](/search?q=audit%5Fauthor.name:Fuentes-Prior, P.), [Iwanaga, Y.](/search?q=audit%5Fauthor.name:Iwanaga, Y.), [Huber, R.](/search?q=audit%5Fauthor.name:Huber, R.), [Pagila, R.](/search?q=audit%5Fauthor.name:Pagila, R.), [Rumennik, G.](/search?q=audit%5Fauthor.name:Rumennik, G.), [Seto, M.](/search?q=audit%5Fauthor.name:Seto, M.), [Morser, J.](/search?q=audit%5Fauthor.name:Morser, J.), [Light, D.R.](/search?q=audit%5Fauthor.name:Light, D.R.), [Bode, W.](/search?q=audit%5Fauthor.name:Bode, W.)
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 - Version 2.2: 2024-05-01
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary - Version 2.3: 2024-11-13
Changes: Structure summary