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SMTL ID : 6zgo.1

Thrombin in complex with D-Phe-Pro-2-chlorofuran derivative (13l)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NA.1:	3 residues within 4Å: Chain B: K.174, D.175, T.177 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.174 Water bridges: B:K.174
NA.2:	2 residues within 4Å: Chain B: R.233, 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

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

NAG.3:

2 residues within 4Å:

Chain B: L.46, N.53

2 PLIP interactions:

2 interactions with chain B

Hydrophobic interactions: B:L.46
Hydrogen bonds: B:N.53

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

DMS.4:	5 residues within 4Å: Chain A: Y.32, I.33 Chain B: S.128, Y.134, F.215 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.134
DMS.5:	6 residues within 4Å: Chain B: L.130, A.132, I.167, V.168, R.170, F.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.170
DMS.7:	5 residues within 4Å: Chain B: R.89, N.91, D.97, R.98, R.180 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 QKE: (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-chloranylfuran-2-yl)methyl]pyrrolidine-2-carboxamide(Non-covalent)

QKE.6:

14 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, A.200, S.205, V.225, S.226, W.227, G.228, G.238, F.239

10 PLIP interactions:

10 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:L.96, B:A.200, B:W.227, B:W.227
Hydrogen bonds: B:S.226, B:G.228, B:G.228

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Sandner, A. et al., Thrombin in complex with D-Phe-Pro-2-chlorofuran derivative (13l). To be published

Release Date

2021-06-30

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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