SMTL ID : 3b9f.1

1.6 A structure of the PCI-thrombin-heparin complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 2 residues within 4Å: Chain B: N.53, T.55 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:K.284, B:N.53 Water bridges: B:N.53, B:N.53, B:N.53

1 x SGN- IDS: 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose(Non-covalent)

SGN-IDS.2: 11 residues within 4Å: Chain B: H.87, P.88, R.89, R.98, N.184, R.245, L.246, K.247, K.248, W.249, K.252 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:P.88 Hydrogen bonds: B:R.89, B:R.89, B:R.89, B:R.98, B:N.184, B:L.246, B:K.248, B:W.249 Water bridges: B:K.252, B:N.184 Salt bridges: B:H.87, B:R.89, B:R.89, B:R.98

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

SO4.3: 4 residues within 4Å: Chain B: R.170, D.183, R.245 Ligands: GOL.4 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.170, B:R.245 SO4.7: 1 residues within 4Å: Chain C: R.370 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.370 Salt bridges: C:R.370 SO4.8: 1 residues within 4Å: Chain C: F.147 No protein-ligand interaction detected (PLIP)

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain B: L.130, I.167, V.168, R.170, C.173, F.186, C.187 Ligands: SO4.3 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.170, B:R.170, B:C.187 Water bridges: B:H.242 GOL.5: 4 residues within 4Å: Chain B: R.70, Y.71, E.72, R.73 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.70, B:Y.71, B:R.73 GOL.6: 6 residues within 4Å: Chain B: R.36, K.104, K.106, P.108, G.258, E.259 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.36, B:K.104, B:E.259 GOL.9: 5 residues within 4Å: Chain B: W.50 Chain C: T.357, F.359, T.360, F.361 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Water bridges: B:E.202, C:T.357, C:F.361 Hydrogen bonds: C:T.357, C:F.361 GOL.10: 6 residues within 4Å: Chain C: D.36, F.37, T.38, S.62, G.83, L.84 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:F.37, C:T.38, C:T.38, C:S.62, C:L.84, C:E.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, W. et al., Molecular basis of thrombin recognition by protein C inhibitor revealed by the 1.6-A structure of the heparin-bridged complex. Proc.Natl.Acad.Sci.Usa (2008)

Release Date

2008-04-22

Peptides

Prothrombin: A
Prothrombin: B
Plasma serine protease inhibitor: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
I

Prothrombin

Prothrombin

Plasma serine protease inhibitor

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