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SMTL ID : 1dx5.1 (3 other biounits)

Crystal structure of the thrombin-thrombomodulin complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1:

3 residues within 4Å:

Chain B: E.13, F.32
Ligands: NA.3

1 PLIP interactions:

1 interactions with chain B

Hydrogen bonds: B:E.13

1 x CA: CALCIUM ION(Non-covalent)

CA.2:

7 residues within 4Å:

Chain B: D.79, I.80, E.82, N.95, L.96, G.98, T.99

5 PLIP interactions:

4 interactions with chain B, 1 Ligand-Water interactions

Metal complexes: B:D.79, B:I.80, B:L.96, B:T.99, H₂O.1

2 x NA: SODIUM ION(Non-functional Binders)

NA.3:	6 residues within 4Å: Chain B: Y.14, C.28, A.29, F.32, C.42 Ligands: FMT.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.29
NA.5:	3 residues within 4Å: Chain C: R.197, D.232, R.233 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.232 Water bridges: C:D.232, C:D.232

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4:

4 residues within 4Å:

Chain C: L.46, P.48, N.53, I.55

2 PLIP interactions:

2 interactions with chain C

Hydrophobic interactions: C:L.46, C:P.48

4 x 0GJ: L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide(Non-covalent)(Covalent)

0GJ.6:	6 residues within 4Å: Chain C: W.148, W.227, G.228, G.230 Ligands: 0GJ.7, 0GJ.8 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.228, C:G.230
0GJ.7:	7 residues within 4Å: Chain C: H.43, L.96, S.226, W.227 Ligands: 0GJ.6, 0GJ.8, 0GJ.9 No protein-ligand interaction detected (PLIP)
0GJ.8:	16 residues within 4Å: Chain C: H.43, D.199, A.200, G.203, D.204, S.205, V.225, S.226, W.227, G.228, G.230, C.231, G.238 Ligands: 0GJ.6, 0GJ.7, 0GJ.9 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:V.225 Hydrogen bonds: C:A.200, C:G.203, C:D.204, C:S.205, C:S.226, C:G.230 Water bridges: C:G.230, C:F.239, C:Y.240 Salt bridges: C:D.199
0GJ.9:	4 residues within 4Å: Chain C: H.43, S.205 Ligands: 0GJ.7, 0GJ.8 No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Fuentes-Prior, P. et al., Structural Basis for the Anticoagulant Activity of the Thrombin-Thrombomodulin Complex. Nature (2000)

Release Date

2000-04-10

Peptides

Thrombin light chain: A
Thrombomodulin: B
Thrombin heavy chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
I

C
M

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Thrombin light chain

Thrombomodulin

Thrombin heavy chain

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