SMTL ID : 3gis.1 (2 other biounits)

Crystal Structure of Na-free Thrombin in Complex with Thrombomodulin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-1-mer

Ligands

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: S.17, G.18, E.19, A.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.18, A:A.20 Water bridges: A:E.19, A:E.19 SO4.2: 2 residues within 4Å: Chain A: N.11, R.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.11 Water bridges: A:R.13 Salt bridges: A:R.13 SO4.3: 5 residues within 4Å: Chain A: F.9 Chain B: D.122, R.123, F.244, K.247 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.123 Salt bridges: B:K.247 SO4.4: 2 residues within 4Å: Chain B: R.98, N.184 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.184 Salt bridges: B:R.98 SO4.5: 4 residues within 4Å: Chain B: A.132, E.169, R.170, P.171 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.170 SO4.6: 2 residues within 4Å: Chain B: W.92, R.93 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.92 Salt bridges: B:R.93 SO4.7: 1 residues within 4Å: Chain B: R.98 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.98 Salt bridges: B:R.98

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 7 residues within 4Å: Chain C: D.79, I.80, E.82, N.95, L.96, G.98, T.99 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.79, C:D.79, C:I.80, C:L.96, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adams, T.E. et al., Molecular basis of thrombomodulin activation of slow thrombin. J.Thromb.Haemost. (2009)

Release Date

2009-08-18

Peptides

Prothrombin: A
Prothrombin: B
Thrombomodulin: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
X

Prothrombin

Prothrombin

Thrombomodulin

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