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SMTL ID : 4dih.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1:	2 residues within 4Å: Chain A: D.8 Chain B: H.116 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.8, A:D.8, B:H.116, H₂O.1
ZN.5:	3 residues within 4Å: Chain B: D.51 Ligands: CL.7, CL.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.51, B:D.51
ZN.6:	2 residues within 4Å: Chain B: R.36, E.82 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.82, B:E.82, H₂O.1, H₂O.1, H₂O.6

1 x 0G6: D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide(Covalent)

0G6.2:

19 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, L.96, I.179, D.199, A.200, C.201, G.203, D.204, S.205, V.225, S.226, W.227, G.228, G.230, C.231, G.238

20 PLIP interactions:

20 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:L.96, B:I.179, B:V.225
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:E.229, B:G.230, B:G.230, B:D.232, B:Y.240
Salt bridges: B:D.199

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

NAG.3:

1 residues within 4Å:

Chain B: N.53

1 PLIP interactions:

1 interactions with chain B

Hydrophobic interactions: B:N.53

2 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:R.233, B:K.236 Water bridges: B:Y.190, B:D.232, B:G.235
NA.9:	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)

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

CL.7:	1 residues within 4Å: Ligands: ZN.5 Ligand excluded by PLIP
CL.8:	2 residues within 4Å: Chain B: D.51 Ligands: ZN.5 Ligand excluded by 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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