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SMTL ID : 6t4a.1

Thrombin in Complex with a D-Phe-Pro-p-aminopyridine derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.31 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1:

3 residues within 4Å:

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

1 PLIP interactions:

1 interactions with chain B

Hydrophobic interactions: B:L.46

1 x J5K: (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(6-azanylpyridin-3-yl)methyl]pyrrolidine-2-carboxamide(Non-covalent)

J5K.2:

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, S.205, V.225, S.226, W.227, G.228, E.229, G.230, C.231
Ligands: GOL.4

13 PLIP interactions:

13 interactions with chain B

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

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

PO4.3:

6 residues within 4Å:

Chain B: R.89, N.91, N.95, D.97, R.98, R.180

8 PLIP interactions:

8 interactions with chain B

Hydrogen bonds: B:N.91, B:D.97
Water bridges: B:R.89, B:R.89, B:R.180, B:R.180
Salt bridges: B:R.98, B:R.180

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4:

9 residues within 4Å:

Chain B: L.27, C.28, H.43, W.50, K.52, E.202, G.203, S.205
Ligands: J5K.2

4 PLIP interactions:

4 interactions with chain B

Hydrogen bonds: B:L.27, B:G.203, B:S.205, B:S.205

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

NA.5:	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:R.197, B:G.235, B:G.238
NA.6:	1 residues within 4Å: Chain B: F.215 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.215

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Ngo, K. et al., Protein-Induced Change in Ligand Protonation during Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins?. J.Med.Chem. (2020)

Release Date

2020-05-13

Peptides

Prothrombin: A
Prothrombin: 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

Prothrombin

Prothrombin

Hirudin variant-2

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