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SMTL ID : 3u8t.1

Human thrombin complexed with D-Phe-Pro-D-Arg-Cys

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

hetero-1-1-mer

Ligands

1 x DPN- PRO- DAR- CYS- NH2: D-PHE-PRO-D-ARG-CYS DIRECT THROMBIN INHIBITOR(Non-covalent)

DPN-PRO-DAR-CYS-NH2.1:

20 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, I.179, D.199, A.200, C.201, E.202, G.203, S.205, V.225, S.226, W.227, G.228, G.230, C.231, G.238

21 PLIP interactions:

21 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:H.43, B:A.200, B:G.203, B:S.205, B:S.226, B:G.228, B:G.228, B:G.230
Water bridges: B:L.27, B:K.52, B:K.52, B:D.232, B:F.239, B:Y.240
Salt bridges: B:D.199

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

NAG.2:

2 residues within 4Å:

Chain B: L.46, N.53

2 PLIP interactions:

2 interactions with chain B

Hydrophobic interactions: B:L.46
Hydrogen bonds: B:N.53

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

NA.3:

3 residues within 4Å:

Chain B: D.232, R.233, K.236

3 PLIP interactions:

3 interactions with chain B

Hydrogen bonds: B:K.236, B:K.236
Water bridges: B:D.234

1 x IOD: IODIDE ION(Non-functional Binders)

IOD.4:

1 residues within 4Å:

Chain B: M.80

Ligand excluded by PLIP

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5:

2 residues within 4Å:

Chain B: H.87, W.249

Ligand excluded by PLIP

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6:

3 residues within 4Å:

Chain B: Y.134, P.214, F.215

2 PLIP interactions:

2 interactions with chain B

Hydrophobic interactions: B:P.214
Hydrogen bonds: B:Y.134

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Figueiredo, A.C. et al., Rational design and characterization of d-phe-pro-d-arg-derived direct thrombin inhibitors. Plos One (2012)

Release Date

2012-04-11

Peptides

Thrombin light chain: A
Thrombin heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

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

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