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SMTL ID : 6tdt.1

Thrombin in Complex with a D-DiPhe-Pro-p-pyridine derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

PO4.1:

7 residues within 4Å:

Chain A: R.89, N.91, N.95, D.97, R.98, R.180, T.182

7 PLIP interactions:

7 interactions with chain A

Hydrogen bonds: A:N.91, A:D.97, A:D.97, A:D.97
Water bridges: A:E.94
Salt bridges: A:R.98, A:R.180

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

NA.2:	4 residues within 4Å: Chain A: K.174, D.175, T.177, R.178 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.174
NA.3:	6 residues within 4Å: Chain A: D.232, R.233, D.234, G.235, K.236, Y.237 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.236, A:K.236 Water bridges: A:G.235, A:G.238

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4:

7 residues within 4Å:

Chain A: L.130, Q.131, A.132, I.167, V.168, R.170, F.186

1 PLIP interactions:

1 interactions with chain A

Hydrogen bonds: A:R.170

1 x LXW: (2~{S})-1-[(2~{R})-2-azanyl-3,3-diphenyl-propanoyl]-~{N}-(pyridin-4-ylmethyl)pyrrolidine-2-carboxamide(Non-covalent)

LXW.5:

17 residues within 4Å:

Chain A: H.43, Y.47, W.50, E.94, N.95, L.96, I.179, A.200, C.201, E.202, S.205, V.225, S.226, W.227, G.228, E.229, G.230

12 PLIP interactions:

12 interactions with chain A

Hydrophobic interactions: A:Y.47, A:W.50, A:L.96, A:L.96, A:I.179, A:V.225, A:W.227, A:E.229
Hydrogen bonds: A:E.202, A:S.226, A:G.228
Water bridges: A:E.229

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

NAG.6:

4 residues within 4Å:

Chain A: L.46, P.48, N.53, W.92

2 PLIP interactions:

2 interactions with chain A

Hydrophobic interactions: A:P.48
Hydrogen bonds: A:N.53

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
H

B
L

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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Background

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