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SMTL ID : 3qlp.1

X-ray structure of the complex between human alpha thrombin and a modified thrombin binding aptamer (mTBA)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 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:

18 residues within 4Å:

Chain A: H.43, Y.47, W.50, 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, C.231, G.238

16 PLIP interactions:

16 interactions with chain A

Hydrophobic interactions: A:Y.47, A:L.96, A:L.96, A:I.179, A:W.227
Hydrogen bonds: A:A.200, A:G.203, A:S.205, A:S.226, A:W.227, A:G.228, A:G.228, A:G.230
Water bridges: A:G.230, A:G.230
Salt bridges: A:D.199

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2:

1 residues within 4Å:

Chain A: N.53

No protein-ligand interaction detected (PLIP)

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

NA.3:

3 residues within 4Å:

Chain A: D.232, R.233, K.236

4 PLIP interactions:

4 interactions with chain A

Hydrogen bonds: A:K.236, A:K.236
Water bridges: A:G.235, A:G.238

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

K.4:	9 residues within 4Å: Chain C: G.1, G.2, G.5, G.6, G.8, G.10, G.11, G.14, G.15 No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Russo Krauss, I. et al., Thrombin-aptamer recognition: a revealed ambiguity. Nucleic Acids Res. (2011)

Release Date

2011-10-19

Peptides

Thrombin heavy chain: A
Thrombin light chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Thrombin heavy chain

Thrombin light chain

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