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SMTL ID : 7ntu.1 (1 other biounit)

X-ray structure of the complex between human alpha thrombin and two duplex/quadruplex aptamers: NU172 and HD22_27mer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 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:

19 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, N.95, 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:L.96, B:I.179, B:W.227
Hydrogen bonds: B:A.200, B:G.203, B:D.204, B:S.205, B:S.226, B:G.228, B:G.228, B:G.230
Salt bridges: B:D.199

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

NAG.2:

2 residues within 4Å:

Chain B: L.46, N.53

2 PLIP interactions:

2 interactions with chain B

Hydrophobic interactions: B:L.46
Hydrogen bonds: B:N.53

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

NA.3:	9 residues within 4Å: Chain C: A.6, G.7, G.8, G.11, G.12, G.16, G.17, G.20, G.21 No protein-ligand interaction detected (PLIP)
NA.4:	8 residues within 4Å: Chain D: G.5, G.7, G.8, G.11, G.12, G.16, G.17, G.20 No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Troisi, R. et al., Structural and functional analysis of the simultaneous binding of two duplex/quadruplex aptamers to human alpha-thrombin. Int.J.Biol.Macromol. (2021)

Release Date

2021-04-28

Peptides

Prothrombin: A
Prothrombin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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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