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SMTL ID : 6z8w.1

X-ray structure of the complex between human alpha thrombin and a thrombin binding aptamer variant (TBA-3G), which contains 1-beta-D-glucopyranosyl residue in the side chain of Thy3 at N3.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 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, G.203, D.204, S.205, V.225, S.226, W.227, G.228, 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:L.96, B:I.179, B:V.225, B:W.227
Hydrogen bonds: B:A.200, B:E.202, 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:D.232, B:Y.240
Salt bridges: B:D.199

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

NA.2:

3 residues within 4Å:

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

5 PLIP interactions:

5 interactions with chain B

Hydrogen bonds: B:Y.190, B:K.236
Water bridges: B:D.234, B:G.235, B:G.238

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

K.3:	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)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Smirnov, I. et al., Expanding the recognition interface of the thrombin-binding aptamer HD1 through modification of residues T3 and T12. Mol Ther Nucleic Acids (2021)

Release Date

2021-01-27

Peptides

Prothrombin: A
Prothrombin: 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

Prothrombin

Prothrombin

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