SMTL ID : 6z8x.1

X-ray structure of the complex between human alpha thrombin and a thrombin binding aptamer variant (TBA-3Leu), which contains leucyl amide in the side chain of Thy3 at N3.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.53 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: 17 residues within 4Å: Chain B: H.43, Y.47, W.50, E.94, L.96, D.199, A.200, C.201, E.202, G.203, S.205, V.225, S.226, W.227, G.228, G.230, G.238 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.47, B:W.50, B:W.50, B:L.96, B:L.96, B:W.227 Hydrogen bonds: B:H.43, B:G.203, B:D.204, B:S.205, B:G.228, B:G.228, B:G.230 Salt bridges: B:D.199, B:E.202

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

NA.2: 6 residues within 4Å: Chain B: Y.190, G.198, D.199, D.232, R.233, K.236 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.190, B:D.199, B:D.232

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

Prothrombin

Prothrombin

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