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SMTL ID : 2ziq.1

Thrombin Inhibition

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x 26U: N-(4-carbamimidoylbenzyl)-1-(4-methylpentanoyl)-L-prolinamide(Non-covalent)

26U.1:

16 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, D.199, A.200, S.205, V.225, S.226, W.227, G.228, G.230, C.231, G.238

10 PLIP interactions:

10 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:V.225, B:W.227
Hydrogen bonds: B:D.199, B:A.200, B:S.226, B:G.228, B:G.230
Water bridges: B:D.232

2 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.235
NA.3:	2 residues within 4Å: Chain B: K.174, T.177 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.174

1 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.4:

4 residues within 4Å:

Chain B: S.176, E.229, G.235, K.236

3 PLIP interactions:

3 interactions with chain B

Hydrophobic interactions: B:K.236, B:K.236
Hydrogen bonds: B:G.235

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Baum, B. et al., Understanding Thrombin Inhibition. To be Published

Release Date

2009-01-13

Peptides

Thrombin light chain: A
Thrombin heavy chain: B
Hirudin variant-1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
I

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

Hirudin variant-1

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