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SMTL ID : 4i7y.1

Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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:

16 residues within 4Å:

Chain A: H.43, Y.47, L.96, 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

17 PLIP interactions:

17 interactions with chain A

Hydrophobic interactions: A:Y.47, A:L.96, A:L.96, A:W.227
Hydrogen bonds: A:A.200, A:E.202, A:G.203, A:D.204, A:S.205, A:S.226, A:G.228, A:G.228, A:G.230
Water bridges: A:W.227, A:D.232, A:Y.240
Salt bridges: A:D.199

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

NA.2:

3 residues within 4Å:

Chain A: Y.190, R.233, K.236

4 PLIP interactions:

4 interactions with chain A

Hydrogen bonds: A:Y.190, A:K.236
Water bridges: A:Y.190, A:G.238

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

NAG.3:

2 residues within 4Å:

Chain A: L.46, N.53

No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Russo Krauss, I. et al., Duplex-quadruplex motifs in a peculiar structural organization cooperatively contribute to thrombin binding of a DNA aptamer. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-10-16

Peptides

Prothrombin: A
Prothrombin: 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

Prothrombin

Prothrombin

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