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SMTL ID : 3da9.1

Crystal structure of thrombin in complex with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ASP- PHE- GLU- GLU- ILE- PRO- GLY- GLU- PTR: Hirudin peptide(Non-covalent)

ASP-PHE-GLU-GLU-ILE-PRO-GLY-GLU-PTR.1:

14 residues within 4Å:

Chain B: F.19, Q.24, E.25, L.26, L.60, R.62, R.68, T.69, R.70, Y.71, E.76, K.77, I.78, M.80

13 PLIP interactions:

13 interactions with chain B

Hydrophobic interactions: B:F.19, B:L.60, B:Y.71, B:Y.71, B:I.78
Hydrogen bonds: B:T.69, B:Y.71, B:Y.71, B:I.78, B:I.78
Water bridges: B:Q.24
Salt bridges: B:R.68, B:K.77

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

NA.2:

2 residues within 4Å:

Chain B: R.233, K.236

3 PLIP interactions:

3 interactions with chain B

Hydrogen bonds: B:K.236, B:K.236
Water bridges: B:G.238

1 x 44U: beta-phenyl-D-phenylalanyl-N-propyl-L-prolinamide(Non-covalent)

44U.3:

14 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, I.179, C.201, S.205, V.225, S.226, W.227, G.228, E.229

12 PLIP interactions:

12 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:L.96, B:I.179, B:I.179, B:V.225, B:W.227, B:E.229
Hydrogen bonds: B:S.226, B:G.228, B:G.228

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Nilsson, M. et al., Compounds binding to the S2-S3 pockets of thrombin. J.Med.Chem. (2009)

Release Date

2009-05-19

Peptides

Thrombin light chain: A
Thrombin heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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

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