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SMTL ID : 6gn7.1

X-ray structure of the complex between human alpha thrombin and NU172, a duplex/quadruplex 26-mer DNA aptamer, in the presence of sodium ions.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG-GAL-SIA.1:

3 residues within 4Å:

Chain B: L.46, N.53, T.55

No protein-ligand interaction detected (PLIP)

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, 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

19 PLIP interactions:

19 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, 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
Water bridges: B:W.227, B:G.230, B:G.230, B:D.232, B:Y.240
Salt bridges: B:D.199

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

NA.3:	2 residues within 4Å: Chain B: R.233, K.236 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.236, B:K.236 Water bridges: B:G.235
NA.4:	8 residues within 4Å: Chain C: G.7, G.8, G.11, G.12, G.16, G.17, G.20, G.21 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5:

4 residues within 4Å:

Chain B: I.9, V.159
Chain C: G.13, G.18

No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Troisi, R. et al., Several structural motifs cooperate in determining the highly effective anti-thrombin activity of NU172 aptamer. Nucleic Acids Res. (2018)

Release Date

2018-10-17

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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1a2c.1 | 1a3b.1 | 1a3e.1 | 1a46.1 | 1a4w.1 | 1a5g.1 | 1a61.1 | 1abi.1 | 1abj.1 | 1ad8.1 | 1ae8.1 | 1afe.1 | 1aht.1 | 1ai8.1 | 1aix.1 | 1awf.1 | 1awh.1 | 1awh.2 | 1ay6.1 | 1b5g.1 | 1b7x.1 | 1ba8.1 | 1bb0.1 | 1bcu.1 | 1bmm.1 | 1bmn.1 | 1bth.1 | 1bth.2 | 1c1u.1 | 1c1v.1 more...less...

1c1w.1 | 1c4u.1 | 1c4v.1 | 1c4y.1 | 1c5l.1 | 1c5n.1 | 1c5o.1 | 1ca8.1 | 1d3p.1 | 1d3q.1 | 1d3t.1 | 1d4p.1 | 1de7.1 | 1de7.2 | 1dit.1 | 1dwb.1 | 1dwc.1 | 1dwd.1 | 1dwe.1 | 1dx5.1 | 1dx5.2 | 1dx5.3 | 1dx5.4 | 1e0f.1 | 1fpc.1 | 1fph.1 | 1g30.1 | 1g32.1 | 1ghv.1 | 1ghw.1 | 1ghx.1 | 1ghy.1 | 1ghy.2 | 1gj4.1 | 1gj5.1 | 1hah.1 | 1hai.1 | 1hao.1 | 1hap.1 | 1hbt.1 | 1hdt.1 | 1hgt.1 | 1hlt.1 | 1hut.1 | 1hxe.1 | 1hxf.1 | 1ihs.1 | 1iht.1 | 1k21.1 | 1k22.1 | 1kts.1 | 1ktt.1 | 1lhc.1 | 1lhd.1 | 1lhe.1 | 1lhf.1 | 1lhg.1 | 1mu6.1 | 1mu8.1 | 1mue.1 | 1no9.1 | 1nrn.1 | 1nro.1 | 1nrp.1 | 1nrq.1 | 1nrr.1 | 1nrs.1 | 1nu7.1 | 1nu7.2 | 1ny2.1 | 1nzq.1 | 1o0d.1 | 1o0d.2 | 1o2g.1 | 1o5g.1 | 1ook.1 | 1oyt.1 | 1p8v.1 | 1ppb.1 | 1qbv.1 | 1qhr.1 | 1qj1.1 | 1qj6.1 | 1qj7.1 | 1rd3.1 | 1rd3.2 | 1rd3.3 | 1riw.1 | 1sfq.1 | 1sfq.2 | 1sg8.1 | 1sg8.2 | 1sg8.3 | 1sgi.1 | 1sgi.2 | 1shh.1 | 1shh.2 | 1sr5.1 | 1t4u.1 | 1t4v.1 | 1tbz.1 | 1thp.1 | 1thr.1 | 1ths.1 | 1ths.2 | 1tmb.1 | 1tmt.1 | 1tmu.1 | 1tom.1 | 1uma.1 | 1uvs.1 | 1w7g.1 | 1way.1 | 1wbg.1 | 1xmn.1 | 1xmn.2 | 1xmn.3 | 1xmn.4 | 1xmn.5 | 2a2x.1 | 2a2x.2 | 2a45.1 | 2afq.1 | 2ank.1 | 2anm.1 | 2bvr.1 | 2bvs.1 | 2bvx.1 | 2bxt.1 | 2bxu.1 | 2c8w.1 | 2c8x.1 | 2c8y.1 | 2c8z.1 | 2c90.1 | 2c93.1 | 2feq.1 | 2feq.2 | 2fes.1 | 2gde.1 | 2gp9.1 | 2h9t.1 | 2hgt.1 | 2hnt.1 | 2hpp.1 | 2hpq.1 | 2hwl.1 | 2jh0.1 | 2jh5.1 | 2jh6.1 | 2od3.1 | 2pgb.1 | 2r2m.1 | 2thf.1 | 2uuf.1 | 2uuj.1 | 2uuk.1 | 2zc9.1 | 2zda.1 | 2zdv.1 | 2zf0.1 | 2zff.1 | 2zfp.1 | 2zfq.1 | 2zfr.1 | 2zg0.1 | 2zgb.1 | 2zgx.1 | 2zhe.1 | 2zhf.1 | 2zhq.1 | 2zhw.1 | 2zi2.1 | 2ziq.1 | 2znk.1 | 2zo3.1 | 3b23.1 | 3bf6.1 | 3c27.1 | 3d49.1 | 3da9.1 | 3dhk.1 | 3dt0.1 | 3dux.1 | 3e6p.1 | 3ee0.1 | 3egk.1 | 3eq0.1 | 3f68.1 | 3gic.1 | 3hat.1 | 3jz1.1 | 3jz1.2 | 3jz2.1 | 3ldx.1 | 3p17.1 | 3p6z.1 | 3p6z.2 | 3p70.1 | 3p70.2 | 3p70.3 | 3p70.4 | 3pmh.1 | 3qlp.1 | 3qto.1 | 3qtv.1 | 3qwc.1 | 3qx5.1 | 3rlw.1 | 3rly.1 | 3rm0.1 | 3rm2.1 | 3rml.1 | 3rmm.1 | 3rmn.1 | 3rmo.1 | 3sha.1 | 3shc.1 | 3si3.1 | 3si4.1 | 3sv2.1 | 3t5f.1 | 3tu7.1 | 3u69.1 | 3u8o.1 | 3u8r.1 | 3u8t.1 | 3u98.1 | 3u9a.1 | 3utu.1 | 3uwj.1 | 3vxe.1 | 3vxf.1 | 4bah.1 | 4bak.1 | 4bam.1 | 4ban.1 | 4bao.1 | 4baq.1 | 4boh.1 | 4boh.2 | 4ch2.1 | 4ch2.2 | 4ch8.1 | 4ch8.2 | 4ch8.3 | 4ch8.4 | 4dih.1 | 4dii.1 | 4e05.1 | 4e06.1 | 4e7r.1 | 4e7r.2 | 4htc.1 | 4htc.2 | 4i7y.1 | 4lxb.1 | 4lz1.1 | 4lz4.1 | 4lz4.2 | 4thn.1 | 4ud9.1 | 4yes.1 | 5cmx.1 | 5do4.1 | 5e8e.1 | 5ew1.1 | 5ew2.1 | 5gds.1 | 5gim.1 | 5jfd.1 | 5jzy.1 | 5l6n.1 | 5lce.1 | 5lpd.1 | 5mjt.1 | 5mls.1 | 5mm6.1 | 5nhu.1 | 5nhu.2 | 5nhu.3 | 6cym.1 | 6cym.2 | 6eo6.1 | 6eo7.1 | 6eo8.1 | 6eo9.1 | 6evv.1 | 6gbw.1 | 6gwe.1 | 6gwe.2 | 6hsx.1 | 6i51.1 | 6pxj.1 | 6pxj.2 | 6rot.1 | 6t3m.1 | 6t3q.1 | 6t4a.1 | 6t52.1 | 6t53.1 | 6t54.1 | 6t55.1 | 6t56.1 | 6t57.1 | 6t7h.1 | 6t7h.2 | 6t89.1 | 6t8a.1 | 6tdt.1 | 6tkg.1 | 6tkh.1 | 6tki.1 | 6tkj.1 | 6tkl.1 | 6v64.1 | 6y02.1 | 6y9h.1 | 6yb6.1 | 6yhg.1 | 6yhj.1 | 6ymp.1 | 6yn3.1 | 6yqv.1 | 6ysj.1 | 6ysx.1 | 6z48.1 | 6z48.2 | 6z48.3 | 6z48.4 | 6z8v.1 | 6z8w.1 | 6z8x.1 | 6zgo.1 | 6zuh.1 | 6zun.1 | 6zuu.1 | 6zuw.1 | 6zux.1 | 6zv7.1 | 6zv8.1 | 7ac9.1 | 7kme.1 | 7mj5.1 | 7mj5.2 | 7mj5.3 | 7mj5.4 | 7mj5.5 | 7mj5.6 | 7ntu.1 | 7ntu.2 | 7phx.1 | 7zkl.1 | 7zkm.1 | 7zkn.1 | 7zkn.2 | 7zko.1 | 8ase.1 | 8ase.2 | 8asf.1 | 8asf.2 | 8bw5.1 | 8kme.1

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