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SMTL ID : 4bao.1

Thrombin in complex with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1:

4 residues within 4Å:

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

No protein-ligand interaction detected (PLIP)

1 x MVF: (2S)-1-[(2R)-2-[(2-azanyl-2-oxidanylidene-ethyl)amino]-2-cyclohexyl-ethanoyl]-N-[(4-carbamimidoylphenyl)methyl]azetidine-2-carboxamide(Non-covalent)

MVF.2:

19 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, 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, C.231, G.238

20 PLIP interactions:

20 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:I.179, B:I.179, B:V.225, B:W.227, B:W.227, B:E.229
Hydrogen bonds: B:D.199, B:A.200, B:E.202, B:S.205, B:S.226, B:G.228, B:G.228, B:G.230
Water bridges: B:W.227, B:D.232, B:Y.240

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

NA.3:	2 residues within 4Å: Chain B: K.174, T.177 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.177
NA.4:	2 residues within 4Å: Chain B: R.233, K.236 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.236, B:K.236 Water bridges: B:G.238

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Winquist, J. et al., Identification of Structure-Kinetic and Structure-Thermodynamic Relationships for Thrombin Inhibitors. Biochemistry (2013)

Release Date

2013-01-16

Peptides

THROMBIN LIGHT CHAIN: A
THROMBIN HEAVY CHAIN: B
HIRUDIN VARIANT-2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

THROMBIN LIGHT CHAIN

THROMBIN HEAVY CHAIN

HIRUDIN VARIANT-2

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