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SMTL ID : 6t54.1

Thrombin in Complex with a D-Phe-Pro-2-bromothiophene Derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NA.1:	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:K.236, B:K.236 Water bridges: B:G.235, B:G.238
NA.2:	4 residues within 4Å: Chain B: K.174, D.175, T.177, R.178 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.177 Water bridges: B:K.174

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

DMS.3:	7 residues within 4Å: Chain B: L.130, Q.131, A.132, I.167, V.168, R.170, F.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.170
DMS.4:	7 residues within 4Å: Chain B: R.89, N.91, N.95, D.97, R.98, R.180, T.182 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.91, B:D.97, B:R.98, B:R.180 Water bridges: B:R.180 Salt bridges: B:D.97

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5:

3 residues within 4Å:

Chain B: D.175, S.176, G.235

1 PLIP interactions:

1 interactions with chain B

Hydrogen bonds: B:D.175

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

NAG.6:

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 MJK: (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-bromanylthiophen-2-yl)methyl]pyrrolidine-2-carboxamide(Non-covalent)

MJK.7:

19 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, G.238

12 PLIP interactions:

12 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:I.179, B:W.227
Hydrogen bonds: B:E.202, B:S.205, B:S.226, B:G.228, B:G.228
Water bridges: B:G.230
Halogen bonds: B:D.199

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Ngo, K. et al., Thrombin in Complex with a D-Phe-Pro-2-bromothiophene Derivative. To Be Published

Release Date

2020-11-18

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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