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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

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 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.236
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

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Thrombin light chain

Thrombin heavy chain

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1a2c.1 | 1a3b.1 | 1a3e.1 | 1a46.1 | 1a4w.1 | 1a5g.1 | 1a61.1 | 1abi.1 | 1abj.1 | 1ad8.1 | 1ae8.1 | 1afe.1 | 1aht.1 | 1ai8.1 | 1aix.1 | 1awf.1 | 1awh.1 | 1awh.2 | 1ay6.1 | 1b5g.1 | 1b7x.1 | 1ba8.1 | 1bb0.1 | 1bcu.1 | 1bmm.1 | 1bmn.1 | 1bth.1 | 1bth.2 | 1c1u.1 | 1c1v.1 more...less...

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