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SMTL ID : 4lz1.1

X-ray structure of the complex between human thrombin and the TBA deletion mutant lacking thymine 12 nucleobase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 0G6: D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide(Covalent)

0G6.1:

20 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, I.179, D.199, A.200, C.201, E.202, G.203, D.204, S.205, S.226, W.227, G.228, G.230, C.231, G.238

18 PLIP interactions:

18 interactions with chain B

Hydrophobic interactions: B:Y.47, B:L.96, B:L.96, B:I.179, B:W.227
Hydrogen bonds: B:A.200, B:G.203, B:D.204, B:S.205, B:S.226, B:G.228, B:G.228, B:G.230
Water bridges: B:W.227, B:W.227, B:G.230, B:D.232
Salt bridges: B:D.199

1 x K: POTASSIUM ION(Non-functional Binders)

K.2:	8 residues within 4Å: Chain C: G.1, G.2, G.5, G.6, G.10, G.11, G.14, G.15 No protein-ligand interaction detected (PLIP)

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

NAG.3:

3 residues within 4Å:

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

2 PLIP interactions:

2 interactions with chain B

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

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

NA.4:

3 residues within 4Å:

Chain B: Y.190, R.233, K.236

5 PLIP interactions:

5 interactions with chain B

Hydrogen bonds: B:K.236, B:K.236
Water bridges: B:R.197, B:G.235, B:G.238

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Pica, A. et al., Dissecting the contribution of thrombin exosite I in the recognition of thrombin binding aptamer. Febs J. (2013)

Release Date

2014-01-08

Peptides

Thrombin light chain: A
Thrombin heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

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

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