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SMTL ID : 3u8r.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

hetero-1-1-mer

Ligands

1 x DPN- PRO- DAR- ILE- NH2: D-Phe-Pro-D-Arg-Ile DERIVED DIRECT THROMBIN INHIBITOR(Non-covalent)

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

25 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, G.238

23 PLIP interactions:

23 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:W.50, B:W.50, B:L.96, B:L.96, B:I.179, B:V.225, B:W.227
Hydrogen bonds: B:H.43, B:A.200, B:E.202, B:S.226, B:G.228, B:G.228, B:G.230
Water bridges: B:E.202, B:E.202, B:S.205, B:W.227, 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, W.92

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:

5 residues within 4Å:

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

5 PLIP interactions:

5 interactions with chain B

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

4 residues within 4Å:

Chain B: H.87, L.246, K.248, W.249

Ligand excluded by PLIP

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

MPD.6:

7 residues within 4Å:

Chain A: Y.26, I.27
Chain B: S.128, L.129, Y.134, P.214, F.215

4 PLIP interactions:

3 interactions with chain B, 1 interactions with chain A

Hydrophobic interactions: B:P.214
Hydrogen bonds: B:Y.134, B:Y.134, A:Y.26

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

MRD.7:

9 residues within 4Å:

Chain B: L.130, Q.131, A.132, I.167, V.168, E.169, R.170, F.186, C.187

3 PLIP interactions:

3 interactions with chain B

Hydrophobic interactions: B:I.167, B:F.186
Hydrogen bonds: B:L.130

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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