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SMTL ID : 3u9a.1

Human Thrombin In Complex With MI330

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1:

2 residues within 4Å:

Chain B: L.46, N.53

No protein-ligand interaction detected (PLIP)

1 x S33: (2S)-N-[[2-(aminomethyl)-5-chloranyl-phenyl]methyl]-1-[(2S)-2-[(3-chloranyl-4-methoxy-phenyl)sulfonylamino]-4-[(4-cyanophenyl)methylamino]-4-oxidanylidene-butanoyl]pyrrolidine-2-carboxamide(Non-covalent)

S33.2:

26 residues within 4Å:

Chain B: H.43, Y.47, W.50, W.92, E.94, N.95, L.96, E.146, 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, R.233, G.238, F.239, Y.240
Ligands: GOL.4

10 PLIP interactions:

10 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:V.225, B:W.227, B:E.229
Hydrogen bonds: B:S.226, B:G.228, B:G.228, B:G.230, B:G.230

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3:	6 residues within 4Å: Chain B: I.167, V.168, R.170, C.173, F.186, C.187 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.168, B:R.170, B:R.170, B:C.187 Water bridges: B:H.242
GOL.4:	7 residues within 4Å: Chain B: L.27, C.28, K.52, E.202, G.203, S.205 Ligands: S33.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.52, B:K.52, B:G.203

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

PO4.5:

4 residues within 4Å:

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

7 PLIP interactions:

7 interactions with chain B

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

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

NA.6:	2 residues within 4Å: Chain B: K.174, T.177 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.174
NA.7:	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

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Biela, A. et al., Thrombin Inhibition. To be Published

Release Date

2012-10-24

Peptides

Thrombin Light Chain: A
Thrombin Heavy Chain: B
Hirudin variant-2: 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-2

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