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SMTL ID : 3u69.1

Unliganded wild-type human thrombin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-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

2 PLIP interactions:

2 interactions with chain B

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

1 x BCN: BICINE(Non-covalent)

BCN.2:

11 residues within 4Å:

Chain B: L.130, Q.131, A.132, I.167, V.168, E.169, R.170, C.173, F.186, C.187, H.242

11 PLIP interactions:

11 interactions with chain B

Hydrogen bonds: B:A.132, B:V.168, B:R.170, B:R.170, B:C.187
Water bridges: B:L.130, B:R.170, B:R.170, B:M.185
Salt bridges: B:R.170, B:H.242

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:

5 residues within 4Å:

Chain B: S.79, M.80, K.106, K.107
Ligands: MRD.6

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:	4 residues within 4Å: Chain B: I.78, S.79, M.80 Ligands: IOD.4 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.78 Hydrogen bonds: B:M.80
MRD.7:	4 residues within 4Å: Chain B: E.124, T.125, S.128, F.215 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.124, B:F.215 Hydrogen bonds: B:S.128

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

MPD.8:

8 residues within 4Å:

Chain B: Y.47, E.94, N.95, L.96, I.179, W.227, G.228, E.229

6 PLIP interactions:

6 interactions with chain B

Hydrophobic interactions: B:L.96, B:L.96, B:I.179, B:I.179, B:W.227, B:E.229

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

Prothrombin: A
Prothrombin: 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

Prothrombin

Prothrombin

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