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SMTL ID : 6yqv.1

Thrombin in complex with 5-chlorothiophene-2-sulfonamide (j94)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 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 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.174

3 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:	5 residues within 4Å: Chain B: E.124, T.125, S.128, F.215 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:F.215
DMS.5:	4 residues within 4Å: Chain B: N.95, L.96, I.179, W.227 No protein-ligand interaction detected (PLIP)

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

PO4.6:

7 residues within 4Å:

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

10 PLIP interactions:

10 interactions with chain B

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

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

NAG.7:

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 8K2: 5-chloranylthiophene-2-sulfonamide(Non-covalent)

8K2.8:

14 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, Y.240

4 PLIP interactions:

4 interactions with chain B

Hydrophobic interactions: B:A.200
Hydrogen bonds: B:G.228, B:G.228
Water bridges: B:G.230

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9:

7 residues within 4Å:

Chain B: D.122, E.124, T.125, F.215, N.216, Y.220
Ligands: DMS.4

2 PLIP interactions:

2 interactions with chain B

Water bridges: B:D.122, B:Y.220

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Scanlan, W. et al., Thrombin in complex with 5-chlorothiophene-2-sulfonamide (j94). To be published

Release Date

2021-04-28

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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Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
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Extreme

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