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SMTL ID : 1riw.1

Thrombin in complex with natural product inhibitor Oscillarin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NAG.1:

3 residues within 4Å:

Chain B: L.46, P.48, N.53

2 PLIP interactions:

2 interactions with chain B

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

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

NA.2:	3 residues within 4Å: Chain C: K.20, D.21, T.23 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.23
NA.3:	4 residues within 4Å: Chain C: Y.36, D.78, R.79, K.82 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.82, C:K.82 Water bridges: C:G.84

1 x OSC: (2R,3AS,6R,7AS)-N-(2-{1-[AMINO(IMINO)METHYL]-2,5-DIHYDRO-1H-PYRROL-3-YL}ETHYL)-6-HYDROXY-1-{N-[(2S)-2-HYDROXY-3-PHENYLPROPANOYL]PHENYLALANYL}OCTAHYDRO-1H-INDOLE-2-CARBOXAMIDE(Non-covalent)

OSC.4:

18 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, E.146
Chain C: D.45, A.46, S.51, V.71, S.72, W.73, G.74, G.76, C.77, R.79, G.84

17 PLIP interactions:

13 interactions with chain C, 4 interactions with chain B

Hydrophobic interactions: C:V.71, C:W.73, B:Y.47, B:W.50, B:L.96
Hydrogen bonds: C:A.46, C:S.72, C:G.74, C:G.74, C:G.76, C:G.76, B:Y.47
Water bridges: C:E.48, C:W.73, C:G.74, C:Y.86
Salt bridges: C:D.45

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Hanessian, S. et al., The N-acyloxyiminium ion aza-Prins route to octahydroindoles: total synthesis and structural confirmation of the antithrombotic marine natural product oscillarin. J.Am.Chem.Soc. (2004)

Release Date

2004-11-09

Peptides

thrombin light chain: A
thrombin heavy chain, B: B
thrombin heavy chain, C: C
Hirudin IIB: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

thrombin light chain

thrombin heavy chain, B

thrombin heavy chain, C

Hirudin IIB

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