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SMTL ID : 3u8o.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.28 Å

Oligo State

hetero-1-1-mer

Ligands

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

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

26 residues within 4Å:

Chain B: L.27, C.28, H.43, C.44, Y.47, W.50, K.52, 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, E.229, G.230, C.231, D.232, G.238

22 PLIP interactions:

22 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:L.96, B:W.227
Hydrogen bonds: B:H.43, B:K.52, B:A.200, B:G.203, B:S.205, B:S.226, B:G.228, B:G.230
Water bridges: B:E.202, B:E.202, B:E.202, B:W.227, B:G.228, B:G.230, B:D.232, B:Y.240
Salt bridges: B:D.199

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

NAG.2:

4 residues within 4Å:

Chain B: L.46, P.48, N.53, T.55

1 PLIP interactions:

1 interactions with chain B

Hydrogen bonds: B:N.53

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

NA.3:

5 residues within 4Å:

Chain B: D.232, R.233, D.234, G.235, K.236

4 PLIP interactions:

4 interactions with chain B

Hydrogen bonds: B:R.233, B:K.236
Water bridges: B:G.235, B:G.238

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

IOD.4:

4 residues within 4Å:

Chain B: S.79, M.80, K.106, K.107

Ligand excluded by PLIP

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

CL.5:

2 residues within 4Å:

Chain B: P.192, D.193

Ligand excluded by PLIP

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.6:	3 residues within 4Å: Chain B: E.124, T.125, F.215 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.215, B:F.215, B:F.215
MRD.7:	6 residues within 4Å: Chain A: Y.26 Chain B: S.128, L.129, Y.134, P.214, F.215 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.129, B:Y.134, B:P.214, B:F.215, B:F.215, A:Y.26

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

2012-05-23

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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