SMTL ID : 8bw5.1

X-ray structure of the complex between human alpha thrombin and the duplex/quadruplex aptamer M08s-1_41mer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- NAG- GAL- SIA- MAN: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-GAL-SIA-MAN.1: 2 residues within 4Å: Chain B: L.46, N.53 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 B: H.43, Y.47, W.50, E.94, 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, G.238 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:I.179, B:W.227 Hydrogen bonds: 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:F.239 Salt bridges: B:D.199

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

NA.3: 3 residues within 4Å: Chain B: D.232, R.233, K.236 No protein-ligand interaction detected (PLIP) NA.4: 9 residues within 4Å: Chain C: G.14, G.15, G.18, G.19, G.20, G.22, G.23, G.26, G.27 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Troisi, R. et al., Steric hindrance and structural flexibility shape the functional properties of a guanine-rich oligonucleotide. Nucleic Acids Res. (2023)

Release Date

2023-07-19

Peptides

Thrombin light chain: A
Thrombin heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

Thrombin light chain

Thrombin heavy chain

Related Entries With Identical Sequence