SMTL ID : 5a2m.1

Thrombin Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: R.178 Ligands: WX5.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.178

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

NA.2: 4 residues within 4Å: Chain A: K.174, D.175, T.177, R.178 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.174 NA.3: 6 residues within 4Å: Chain A: D.232, R.233, D.234, G.235, K.236, Y.237 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.236, A:K.236 Water bridges: A:G.235, A:G.238

1 x WX5: (2S)-1-[(2R)-5-carbamimidamido-2-[(phenylmethyl)sulfonylamino]pentanoyl]-N-[[5-chloranyl-2-(hydroxymethyl)phenyl]methyl]pyrrolidine-2-carboxamide(Non-covalent)

WX5.4: 23 residues within 4Å: Chain A: H.43, Y.47, W.50, L.96, E.146, T.177, I.179, D.199, A.200, C.201, E.202, S.205, V.225, S.226, W.227, G.228, E.229, G.230, C.231, G.238, F.239, Y.240 Ligands: GOL.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.47, A:W.50, A:A.200, A:E.202, A:V.225 Hydrogen bonds: A:S.226, A:G.228, A:G.228, A:G.230 Water bridges: A:T.177, A:E.229 Salt bridges: A:E.229

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

NAG.5: 3 residues within 4Å: Chain A: L.46, P.48, N.53 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruehmann, E. et al., Thrombin Inhibition. To be Published

Release Date

2016-06-01

Peptides

THROMBIN HEAVY CHAIN: A
HIRUDIN VARIANT-2: B
THROMBIN LIGHT CHAIN: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
I

C
L

THROMBIN HEAVY CHAIN

HIRUDIN VARIANT-2

THROMBIN LIGHT CHAIN

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