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SMTL ID : 7zkl.1

X-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (TBA-NNp/DDp) - Crystal form alpha

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.18 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:

20 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, 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, B:L.96, B:I.179, B:W.227
Hydrogen bonds: B:G.203, B:D.204, B:S.205, B:S.226, B:W.227, B:G.228, B:G.228, B:G.230
Water bridges: B:F.239
Salt bridges: B:D.199

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

NA.2:

3 residues within 4Å:

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

2 PLIP interactions:

2 interactions with chain B

Hydrogen bonds: B:R.233, B:R.233

1 x LMR: (2S)-2-hydroxybutanedioic acid(Non-covalent)

LMR.3:

5 residues within 4Å:

Chain B: V.168, E.169, R.170, F.186, R.245

5 PLIP interactions:

5 interactions with chain B

Hydrogen bonds: B:R.170, B:C.187
Salt bridges: B:R.170, B:R.170, B:R.245

1 x JL0: 3-[13-methyl-5,7,12,14-tetrakis(oxidanylidene)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1(15),2,4(16),8,10-pentaen-6-yl]propyl 3-[5,7,12,14-tetrakis(oxidanylidene)-13-(3-oxidanylpropyl)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1,3,8(16),9,11(15)-pentaen-6-yl]propyl hydrogen phosphate(Non-functional Binders)

JL0.4:

7 residues within 4Å:

Chain C: G.1, G.6, T.7, G.8, G.10, G.15
Ligands: JKR.5

No protein-ligand interaction detected (PLIP)

1 x JKR: 3-[5-[3-bis(oxidanyl)phosphanyloxypropoxy]naphthalen-1-yl]oxypropyl 3-(5-oxidanylnaphthalen-1-yl)oxypropyl hydrogen phosphate(Non-functional Binders)

JKR.5:

4 residues within 4Å:

Chain C: T.7, G.8, G.15
Ligands: JL0.4

No protein-ligand interaction detected (PLIP)

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

K.6:	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

Troisi, R. et al., A terminal functionalization strategy reveals unusual binding abilities of anti-thrombin anticoagulant aptamers. Mol Ther Nucleic Acids (2022)

Release Date

2022-11-30

Peptides

Thrombin light chain: A
Thrombin heavy chain: 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

Thrombin light chain

Thrombin heavy chain

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