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SMTL ID : 6ysj.1

Thrombin in complex with 2-amino-1-(4-bromophenyl)ethan-1-one (j10)

Coordinates

PDB Format Compare

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:R.233, 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

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:	4 residues within 4Å: Chain B: E.124, T.125, S.128, F.215 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.128 pi-Cation interactions: B:F.215

2 x 47A: 2-amino-1-(4-bromophenyl)ethanone(Non-covalent)

47A.5:	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 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.200, B:V.225 Hydrogen bonds: B:G.228 Water bridges: B:G.228, B:G.228, B:G.230
47A.6:	9 residues within 4Å: Chain B: Y.47, P.49, W.92, R.93, E.94, N.95, L.96, I.179, W.227 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.96, B:I.179

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

3 PLIP interactions:

3 interactions with chain B

Hydrophobic interactions: B:L.46, B:P.48
Hydrogen bonds: B:N.53

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Scanlan, W. et al., Thrombin in complex with 2-amino-1-(4-bromophenyl)ethan-1-one (j10). To be published

Release Date

2021-05-12

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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