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SMTL ID : 4dii.1

X-ray structure of the complex between human alpha thrombin and thrombin binding aptamer in the presence of potassium ions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1:	2 residues within 4Å: Chain A: D.8 Chain B: H.116 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.116, A:D.8
ZN.5:	3 residues within 4Å: Chain B: D.51 Ligands: CL.6, CL.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.51, B:D.51

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, 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 B

Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:L.96
Hydrogen bonds: B:A.200, B:G.203, B:S.205, B:S.226, B:G.228, B:G.228, B:G.230
Water bridges: B:W.227, B:G.230, B:G.230, B:G.230, B:Y.240
Salt bridges: B:D.199

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

NAG.3:

2 residues within 4Å:

Chain B: N.53, T.55

No protein-ligand interaction detected (PLIP)

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

NA.4:

3 residues within 4Å:

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

5 PLIP interactions:

5 interactions with chain B

Hydrogen bonds: B:K.236, B:K.236
Water bridges: B:D.232, B:G.235, B:G.238

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6:	1 residues within 4Å: Ligands: ZN.5 Ligand excluded by PLIP
CL.7:	2 residues within 4Å: Chain B: D.51 Ligands: ZN.5 Ligand excluded by PLIP

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

K.8:	8 residues within 4Å: Chain C: G.1, G.2, G.5, G.6, 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., High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity. Nucleic Acids Res. (2012)

Release Date

2012-07-18

Peptides

Prothrombin: A
Prothrombin: 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

Prothrombin

Prothrombin

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