SMTL ID : 3dt0.1

Understanding Thrombin Inhibition

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x 16U: N-(3-chlorobenzyl)-1-(4-methylpentanoyl)-L-prolinamide(Non-covalent)

16U.1: 12 residues within 4Å: Chain B: H.43, Y.47, W.50, L.96, A.200, S.205, V.225, S.226, W.227, G.228, G.238, F.239 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:V.225, B:W.227 Hydrogen bonds: B:S.226, B:G.228

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

NA.2: 3 residues within 4Å: Chain B: D.232, R.233, K.236 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.233 Water bridges: B:R.233, B:G.235 NA.3: 2 residues within 4Å: Chain B: K.174, T.177 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.177, B:T.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2009-06-23

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

Thrombin light chain

Thrombin heavy chain

Hirudin variant-1

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