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SMTL ID : 6eo7.1

X-ray structure of the complex between human alpha-thrombin and modified 15-mer DNA aptamer containing 5-(3-(acetamide-N-yl)-1-propen-1-yl)-2'-deoxyuridine residue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

hetero-1-1-mer

Ligands

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

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

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

0G6.2:

18 residues within 4Å:

Chain C: H.43, Y.47, W.50, E.94, L.96, 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

17 PLIP interactions:

17 interactions with chain C

Hydrophobic interactions: C:Y.47, C:L.96, C:L.96, C:W.227
Hydrogen bonds: C:A.200, C:E.202, C:G.203, C:D.204, C:S.205, C:S.226, C:G.228, C:G.228, C:G.230
Water bridges: C:W.227, C:D.232, C:Y.240
Salt bridges: C:D.199

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

NA.3:

3 residues within 4Å:

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

4 PLIP interactions:

4 interactions with chain C

Hydrogen bonds: C:Y.190, C:K.236
Water bridges: C:D.234, C:G.235

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

NAG.4:

1 residues within 4Å:

Chain C: N.53

No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Dolot, R. et al., Crystal structures of thrombin in complex with chemically modified thrombin DNA aptamers reveal the origins of enhanced affinity. Nucleic Acids Res. (2018)

Release Date

2017-10-18

Peptides

Prothrombin: B
Prothrombin: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
L

C
H

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Prothrombin

Prothrombin

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