SMTL ID : 5cmx.1

X-ray structure of the complex between human alpha thrombin and a duplex/quadruplex 31-mer DNA aptamer

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.98 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(Non-covalent)

0G6.1: 18 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, D.204, S.205, S.226, W.227, G.228, E.229, G.230, G.238 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.47, B:W.50, B:L.96 Hydrogen bonds: B:A.200, B:E.202, B:G.203, B:S.205, B:S.205, B:S.226, B:G.228, B:G.228, B:E.229, B:G.230 Water bridges: B:W.227, B:D.232, B:Y.240 Salt bridges: B:D.199, B:E.202

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

K.2: 9 residues within 4Å: Chain C: G.9, G.10, G.13, G.14, G.16, G.18, G.19, G.22, G.23 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Russo Krauss, I. et al., Different duplex/quadruplex junctions determine the properties of anti-thrombin aptamers with mixed folding. Nucleic Acids Res. (2016)

Release Date

2016-01-13

Peptides

alpha thrombin-light chain: A
Thrombin heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

alpha thrombin-light chain

Thrombin heavy chain

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