6i51.1 | SWISS-MODEL Template Library

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SMTL ID : 6i51.1

Thrombin in complex with fragment J02

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1:

5 residues within 4Å:

Chain B: L.46, P.48, N.53, T.55, W.92

2 PLIP interactions:

2 interactions with chain B

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

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

DMS.2:	6 residues within 4Å: Chain B: L.130, Q.131, A.132, I.167, R.170, F.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.170
DMS.3:	4 residues within 4Å: Chain B: E.124, T.125, S.128, F.215 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.128 pi-Cation interactions: B:F.215

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

PO4.4:

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:R.89, B:N.91, B:D.97
Water bridges: B:E.94
Salt bridges: B:R.98, B:R.180

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

NA.5:	4 residues within 4Å: Chain B: K.174, D.175, T.177, R.178 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.174
NA.6:	5 residues within 4Å: Chain B: D.232, R.233, D.234, G.235, K.236 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.236, B:K.236 Water bridges: B:G.235

1 x F05: 1H-isoindol-3-amine(Non-covalent)

F05.7:

13 residues within 4Å:

Chain B: D.199, A.200, C.201, E.202, S.205, V.225, S.226, W.227, G.228, G.230, C.231, G.238, F.239

5 PLIP interactions:

5 interactions with chain B

Hydrophobic interactions: B:V.225
Hydrogen bonds: B:D.199, B:A.200
Water bridges: B:E.229, B:F.239

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Abazi, N. et al., Fragment screening of Thrombin using a 96 member fragment library. To Be Published

Release Date

2019-11-20

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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