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SMTL ID : 5jlg.2 (1 other biounit)

The X-ray structure of the adduct formed in the reaction between bovine pancreatic ribonuclease and compound I, a piano-stool organometallic Ru(II) arene compound containing an O,S-chelating ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

1 x RU: RUTHENIUM ION(Non-covalent)

RU.1:

4 residues within 4Å:

Chain A: H.105
Ligands: 6L6.2, DMS.3, DMS.4

3 PLIP interactions:

1 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions

Metal complexes: A:H.105, H₂O.2, DMS.4

1 x 6L6: methyl (2Z)-3-hydroxy-3-(3-hydroxyphenyl)prop-2-ene(dithioate)(Non-covalent)

6L6.2:

7 residues within 4Å:

Chain A: K.61, Q.74, H.105, V.124
Ligands: RU.1, DMS.3, DMS.4

1 PLIP interactions:

1 interactions with chain A

Hydrophobic interactions: A:V.124

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3:	3 residues within 4Å: Ligands: RU.1, 6L6.2, DMS.4 No protein-ligand interaction detected (PLIP)
DMS.4:	6 residues within 4Å: Chain A: Y.76, T.78, H.105 Ligands: RU.1, 6L6.2, DMS.3 No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Hildebrandt, J. et al., Unusual mode of protein binding by a cytotoxic pi-arene ruthenium(ii) piano-stool compound containing an O,S-chelating ligand. Dalton Trans (2016)

Release Date

2016-08-03

Peptides

Ribonuclease pancreatic: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Ribonuclease pancreatic

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1a2w.1 | 1afk.1 | 1afk.2 | 1afl.1 | 1afl.2 | 1afu.1 | 1afu.2 | 1aqp.1 | 1bel.1 | 1bzq.1 | 1bzq.2 | 1bzq.3 | 1bzq.4 | 1dfj.1 | 1eos.1 | 1eos.2 | 1eow.1 | 1f0v.1 | 1f0v.2 | 1f0v.3 | 1f0v.4 | 1fs3.1 | 1jn4.1 | 1jn4.2 | 1js0.1 | 1jvt.1 | 1jvt.2 | 1jvu.1 | 1jvu.2 | 1jvv.1 more...less...

1jvv.2 | 1kf2.1 | 1kf3.1 | 1kf4.1 | 1kf5.1 | 1kf7.1 | 1kf8.1 | 1o0f.1 | 1o0f.2 | 1o0h.1 | 1o0h.2 | 1o0m.1 | 1o0m.2 | 1o0n.1 | 1o0n.2 | 1o0o.1 | 1o0o.2 | 1qhc.1 | 1qhc.2 | 1rat.1 | 1rbb.1 | 1rbj.1 | 1rbn.1 | 1rbw.1 | 1rbx.1 | 1rca.1 | 1rcn.1 | 1rha.1 | 1rhb.1 | 1rnc.1 | 1rnd.1 | 1rnm.1 | 1rnm.2 | 1rnn.1 | 1rno.1 | 1rnq.1 | 1rnu.1 | 1rnv.1 | 1rnw.1 | 1rnx.1 | 1rny.1 | 1rnz.1 | 1rob.1 | 1rpf.1 | 1rpg.1 | 1rph.1 | 1rsm.1 | 1rta.1 | 1rtb.1 | 1ruv.1 | 1u1b.1 | 1u1b.2 | 1w4o.1 | 1w4o.2 | 1w4p.1 | 1w4p.2 | 1w4q.1 | 1w4q.2 | 1wbu.1 | 1wbu.2 | 1xps.1 | 1xps.2 | 1xpt.1 | 1xpt.2 | 1z6d.1 | 1z6d.2 | 1z6d.3 | 1z6s.1 | 1z6s.2 | 2aas.1 | 2blp.1 | 2blz.1 | 2e33.1 | 2e3w.1 | 2g4w.1 | 2g4w.2 | 2g4x.1 | 2g8q.1 | 2g8q.2 | 2g8r.1 | 2g8r.2 | 2p42.1 | 2p42.2 | 2p43.1 | 2p44.1 | 2p45.1 | 2p46.1 | 2p46.2 | 2p47.1 | 2p48.1 | 2p49.1 | 2p4a.1 | 2p4a.2 | 2qca.1 | 2rat.1 | 2rns.1 | 2w5g.1 | 2w5g.2 | 2w5i.1 | 2w5i.2 | 2w5k.1 | 2w5k.2 | 2w5l.1 | 2w5l.2 | 2w5m.1 | 2w5m.2 | 2xog.1 | 2xog.2 | 2xoi.1 | 2xoi.2 | 3a1r.1 | 3d6o.1 | 3d6o.2 | 3d6p.1 | 3d6p.2 | 3d6q.1 | 3d6q.2 | 3d7b.1 | 3d7b.2 | 3d8y.1 | 3d8y.2 | 3d8z.1 | 3d8z.2 | 3dh5.1 | 3dh5.2 | 3dxg.1 | 3dxg.2 | 3dxh.1 | 3dxh.2 | 3eux.1 | 3eux.2 | 3euy.1 | 3euy.2 | 3euz.1 | 3euz.2 | 3ev0.1 | 3ev0.2 | 3ev1.1 | 3ev1.2 | 3ev2.1 | 3ev2.2 | 3ev3.1 | 3ev3.2 | 3ev4.1 | 3ev4.2 | 3ev5.1 | 3ev5.2 | 3ev6.1 | 3ev6.2 | 3i67.1 | 3i6f.1 | 3i6h.1 | 3i6j.1 | 3i7w.1 | 3jw1.1 | 3jw1.2 | 3lxo.1 | 3lxo.2 | 3qsk.1 | 3rat.1 | 3rn3.1 | 4ao1.1 | 4g8v.1 | 4g8v.2 | 4g8y.1 | 4g8y.2 | 4g90.1 | 4g90.2 | 4j5z.1 | 4j60.1 | 4j61.1 | 4j62.1 | 4j63.1 | 4j64.1 | 4j65.1 | 4j66.1 | 4j67.1 | 4j68.1 | 4j69.1 | 4j6a.1 | 4l55.1 | 4l55.2 | 4mxf.1 | 4mxf.2 | 4ooh.1 | 4ooh.2 | 4ot4.1 | 4ot4.2 | 4peq.1 | 4peq.2 | 4pou.1 | 4qh3.1 | 4qh3.2 | 4rat.1 | 4rte.1 | 4rte.2 | 4s0q.1 | 4s0q.2 | 4s18.1 | 4s18.2 | 4zz4.1 | 5d6u.1 | 5d97.1 | 5e5e.1 | 5e5e.2 | 5e5f.1 | 5e5f.2 | 5jlg.1 | 5jmg.1 | 5jmg.2 | 5jml.1 | 5jml.2 | 5na9.1 | 5nj7.1 | 5nj7.2 | 5obc.1 | 5obc.2 | 5obd.1 | 5obd.2 | 5obe.1 | 5obe.2 | 5ogh.1 | 5old.1 | 5old.2 | 5rat.1 | 5rsa.1 | 6etk.1 | 6etl.1 | 6etm.1 | 6etn.1 | 6eto.1 | 6etp.1 | 6etq.1 | 6etr.1 | 6f60.1 | 6gok.1 | 6gok.2 | 6pvu.1 | 6pvu.2 | 6pvv.1 | 6pvv.2 | 6pvw.1 | 6pvw.2 | 6pvx.1 | 6pvx.2 | 6qe9.1 | 6qe9.2 | 6rat.1 | 6rsa.1 | 6xhc.1 | 6xhc.2 | 6xhd.1 | 6xhd.2 | 6xhe.1 | 6xhe.2 | 6xhf.1 | 6xhf.2 | 6xvx.1 | 6xvx.2 | 6xw0.1 | 6xw0.2 | 6yo1.1 | 6yo1.2 | 7p4r.1 | 7p8r.1 | 7p8r.2 | 7pni.1 | 7pni.2 | 7q75.1 | 7q76.1 | 7q77.1 | 7q78.1 | 7q79.1 | 7q7a.1 | 7q7b.1 | 7qhr.1 | 7qhr.2 | 7qpw.1 | 7qpw.2 | 7qpy.1 | 7qpy.2 | 7qpz.1 | 7qpz.2 | 7qq0.1 | 7qq0.2 | 7qwh.1 | 7qwh.2 | 7r1p.1 | 7r1p.2 | 7rat.1 | 7rsa.1 | 7z6d.1 | 7z6d.2 | 7z6g.1 | 7z6g.2 | 8c3b.1 | 8fhm.1 | 8fhm.2 | 8gc9.1 | 8gc9.2 | 8ggg.1 | 8ggg.2 | 8oqc.1 | 8oqd.1 | 8oqe.1 | 8oqf.1 | 8oqg.1 | 8px0.1 | 8px0.2 | 8rat.1 | 8rsa.1 | 8s96.1 | 8s96.2 | 8uax.1 | 8uax.2 | 8uay.1 | 8uay.2 | 8uaz.1 | 8uaz.2 | 8ub0.1 | 8ub0.2 | 8ub1.1 | 8ub1.2 | 8ub2.1 | 8ub2.2 | 9eo5.1 | 9eo5.2 | 9eo8.1 | 9eo8.2 | 9gys.1 | 9gys.2 | 9jwd.1 | 9jwh.1 | 9rat.1 | 9rsa.1

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