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SMTL ID : 2zda.1

Exploring Thrombin S1 pocket

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NA.1:	3 residues within 4Å: Chain B: Y.190, R.233, K.236 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.236, B:K.236 Water bridges: B:G.235, B:G.238
NA.2:	2 residues within 4Å: Chain B: K.174, T.177 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.177

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3:

4 residues within 4Å:

Chain B: N.91, D.97, R.98, R.180

11 PLIP interactions:

11 interactions with chain B

Hydrogen bonds: B:N.91, B:D.97, B:D.97
Water bridges: B:R.89, B:R.89, B:R.89, B:R.89, B:N.91, B:R.180
Salt bridges: B:R.98, B:R.180

1 x 32U: D-phenylalanyl-N-{4-[amino(iminio)methyl]benzyl}-L-prolinamide(Non-covalent)

32U.4:

17 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, I.179, D.199, A.200, S.205, V.225, S.226, W.227, G.228, G.230, C.231, G.238

14 PLIP interactions:

14 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:I.179, B:V.225, B:W.227
Hydrogen bonds: B:D.199, B:A.200, B:S.226, B:G.228, B:G.228
Water bridges: B:W.227, B:D.232, B:Y.240

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Baum, B. et al., Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin. J.Mol.Biol. (2009)

Release Date

2008-10-28

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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