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SMTL ID : 7m4n.2 (1 other biounit)

Crystal structure of RBR E3 ligase RNF216 in complex with K63-linked di-ubiquitin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

hetero-1-2-mer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1:	4 residues within 4Å: Chain A: C.29, C.32, C.47, C.49 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.29, A:C.32, A:C.47, A:C.49
ZN.2:	4 residues within 4Å: Chain A: C.54, C.57, H.66, C.84 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.54, A:C.57, A:H.66, A:C.84
ZN.3:	4 residues within 4Å: Chain A: C.68, H.70, C.78, C.81 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.68, A:H.70, A:C.78, A:C.81

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.4:	5 residues within 4Å: Chain A: R.25, E.95 Chain B: G.47, K.48, Q.49 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.47, B:Q.49, A:E.95 Salt bridges: A:R.25
SO4.5:	3 residues within 4Å: Chain A: H.70, E.80, R.83 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.70, A:R.83
SO4.7:	2 residues within 4Å: Chain C: R.42, R.72 4 PLIP interactions: 4 interactions with chain C Water bridges: C:R.72, C:R.72 Salt bridges: C:R.42, C:R.72
SO4.8:	4 residues within 4Å: Chain A: S.73, P.74 Chain C: K.48, Y.59 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Water bridges: C:E.51 Salt bridges: C:K.48 Hydrogen bonds: A:S.73

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6:

4 residues within 4Å:

Chain A: S.39, E.40, G.41, D.89

4 PLIP interactions:

4 interactions with chain A

Hydrogen bonds: A:E.40, A:G.41, A:G.41, A:D.89

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Cotton, T.R. et al., Structural basis of K63-ubiquitin chain formation by the Gordon-Holmes syndrome RBR E3 ubiquitin ligase RNF216. Mol.Cell (2022)

Release Date

2022-01-05

Peptides

E3 ubiquitin-protein ligase RNF216: A
Ubiquitin: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
F

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

E3 ubiquitin-protein ligase RNF216

Ubiquitin

Toggle Identical (BC)

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1aar.1 | 1cmx.1 | 1d3z.1 | 1f9j.1 | 1fxt.1 | 1g6j.1 | 1nbf.1 | 1nbf.2 | 1ogw.1 | 1p3q.1 | 1p3q.2 | 1q5w.1 | 1s1q.1 | 1s1q.2 | 1tbe.1 | 1ubi.1 | 1ubq.1 | 1uzx.1 | 1v80.1 | 1v81.1 | 1wr6.1 | 1wr6.2 | 1wr6.3 | 1wr6.4 | 1wrd.1 | 1wrd.2 | 1xqq.1 | 1yd8.1 | 1yd8.2 | 2ayo.1 more...less...

2ayo.2 | 2bgf.1 | 2c7m.1 | 2c7n.1 | 2c7n.2 | 2c7n.3 | 2c7n.4 | 2c7n.5 | 2c7n.6 | 2d3g.1 | 2den.1 | 2dx5.1 | 2fid.1 | 2fif.1 | 2fif.2 | 2fif.3 | 2fuh.1 | 2g45.1 | 2g45.2 | 2gmi.1 | 2hd5.1 | 2hth.1 | 2jf5.1 | 2jri.1 | 2jy6.1 | 2jzz.1 | 2k39.1 | 2k8b.1 | 2k8c.1 | 2kde.1 | 2kdf.1 | 2klg.1 | 2kn5.1 | 2kox.1 | 2ktf.1 | 2kwu.1 | 2kwv.1 | 2l0f.1 | 2l0t.1 | 2l3z.1 | 2lj5.1 | 2lvo.1 | 2lvp.1 | 2lvq.1 | 2lz6.1 | 2mbh.1 | 2mbo.1 | 2mbq.1 | 2mcn.1 | 2mj5.1 | 2mjb.1 | 2mor.1 | 2mro.1 | 2n3u.1 | 2n3v.1 | 2n3w.1 | 2nr2.1 | 2o6v.1 | 2o6v.2 | 2o6v.3 | 2oob.1 | 2pe9.1 | 2pea.1 | 2qho.1 | 2qho.2 | 2qho.3 | 2qho.4 | 2rr9.1 | 2wwz.1 | 2wx0.1 | 2wx0.2 | 2wx1.1 | 2xbb.1 | 2xbb.2 | 2xew.1 | 2xew.2 | 2xew.3 | 2xk5.1 | 2z59.1 | 2zcc.1 | 2zcc.2 | 2zcc.3 | 2zcc.4 | 3a33.1 | 3alb.1 | 3aul.1 | 3eec.1 | 3eec.2 | 3eec.3 | 3eec.4 | 3efu.1 | 3ehv.1 | 3ehv.2 | 3ehv.3 | 3h1u.1 | 3h1u.2 | 3h7p.1 | 3h7s.1 | 3h7s.2 | 3h7s.3 | 3hm3.1 | 3hm3.2 | 3hm3.3 | 3hm3.4 | 3m3j.1 | 3m3j.2 | 3m3j.3 | 3mhs.1 | 3n30.1 | 3n30.2 | 3n32.1 | 3nhe.1 | 3ns8.1 | 3ns8.2 | 3ns8.3 | 3ofi.1 | 3ofi.2 | 3phd.1 | 3tbl.1 | 3tmp.1 | 3tmp.2 | 3tmp.3 | 3tmp.4 | 3ugb.1 | 3vht.1 | 3vuw.1 | 3vuw.2 | 3vuw.3 | 3vux.1 | 3vux.2 | 3vux.3 | 3vuy.1 | 3vuy.2 | 3vuy.3 | 4bbn.1 | 4bos.1 | 4boz.1 | 4boz.2 | 4boz.3 | 4bvu.1 | 4ddg.1 | 4ddg.2 | 4ddi.1 | 4dhj.1 | 4dhj.2 | 4dhj.4 | 4dhj.5 | 4dhz.1 | 4jqw.1 | 4k7s.1 | 4k7s.2 | 4k7s.3 | 4k7u.1 | 4k7u.2 | 4k7u.3 | 4k7w.1 | 4k7w.2 | 4k7w.3 | 4ldt.1 | 4ljo.1 | 4ljp.1 | 4m0w.1 | 4mm3.1 | 4s1z.1 | 4s1z.2 | 4s1z.3 | 4s1z.4 | 4s1z.5 | 4s22.1 | 4s22.2 | 4un2.1 | 4wlr.1 | 4wur.1 | 4wzp.1 | 4wzp.2 | 4wzp.3 | 4wzp.4 | 4wzp.5 | 4wzp.6 | 4wzp.7 | 4wzp.8 | 4xkh.1 | 4xkh.2 | 4xkh.3 | 4xof.1 | 4xok.1 | 4xok.2 | 4xok.3 | 4xol.1 | 4xol.2 | 4xyz.1 | 4y1h.1 | 4z9s.1 | 4zux.1 | 4zux.2 | 5a5b.1 | 5ait.1 | 5aiu.1 | 5bz0.1 | 5d0k.1 | 5d0k.2 | 5d0k.3 | 5d0k.4 | 5d0m.1 | 5dfl.1 | 5edv.1 | 5edv.2 | 5edv.3 | 5eya.1 | 5fer.1 | 5gjq.1 | 5go7.1 | 5go8.1 | 5gob.1 | 5goc.1 | 5god.1 | 5gog.1 | 5goh.1 | 5goi.1 | 5goj.1 | 5gok.1 | 5h7s.1 | 5j8p.1 | 5jbv.1 | 5jby.1 | 5jqs.1 | 5jtj.1 | 5jtj.2 | 5jtv.1 | 5jtv.2 | 5jtv.3 | 5jtv.4 | 5jtv.5 | 5jtv.6 | 5jtv.7 | 5k9p.1 | 5kgf.1 | 5kyc.1 | 5kyd.1 | 5kye.1 | 5kye.2 | 5kyf.1 | 5mn9.1 | 5nmc.1 | 5nmc.2 | 5nmc.3 | 5nvg.1 | 5ohl.1 | 5ohl.2 | 5ohl.3 | 5ohl.4 | 5ohl.5 | 5ohl.6 | 5ohl.7 | 5ohp.1 | 5ohv.1 | 5tut.1 | 5txk.1 | 5ujl.1 | 5ujn.1 | 5ulf.1 | 5ulf.2 | 5ulh.1 | 5ulk.1 | 5v1y.1 | 5v1y.2 | 5v1z.1 | 5v1z.2 | 5vey.1 | 5vf0.1 | 5vnz.1 | 5vnz.2 | 5vo0.1 | 5vzm.1 | 5wfi.1 | 5wfi.2 | 5x3m.1 | 5x3n.1 | 5x3o.1 | 5xbo.1 | 5xdp.2 | 5xiu.1 | 5xk4.1 | 5xk5.1 | 5xpk.1 | 5xu8.1 | 5xve.1 | 5ymy.1 | 5zbu.2 | 6aqr.1 | 6asr.1 | 6asr.2 | 6b7m.1 | 6b7o.1 | 6djx.1 | 6e2b.1 | 6ftx.1 | 6if1.1 | 6if1.2 | 6isu.1 | 6jb6.1 | 6jb7.1 | 6jma.1 | 6jwi.1 | 6k9p.1 | 6kl4.1 | 6kow.1 | 6kox.1 | 6lp2.1 | 6n13.1 | 6nxk.1 | 6nxk.2 | 6oi4.1 | 6oi4.2 | 6p5b.1 | 6q00.1 | 6q01.1 | 6q01.2 | 6qml.1 | 6qml.2 | 6rya.1 | 6rya.2 | 6rya.3 | 6s53.1 | 6s53.2 | 6sqr.1 | 6t9l.1 | 6tbm.1 | 6tnf.1 | 6ttu.1 | 6tuv.1 | 6tuv.2 | 6txb.1 | 6txb.2 | 6v5d.1 | 6vae.1 | 6vaf.1 | 6w9d.1 | 6w9d.2 | 6w9d.3 | 6wjd.1 | 6wtg.1 | 6z7v.1 | 7bbd.1 | 7bbf.1 | 7cap.1 | 7dni.1 | 7dnj.1 | 7f0u.1 | 7f0u.2 | 7f7x.1 | 7jxv.1 | 7keo.1 | 7keo.2 | 7m4m.1 | 7m4m.2 | 7m4n.1 | 7m4o.1 | 7myf.2 | 7npi.1 | 7npi.2 | 7npi.3 | 7npi.4 | 7npi.5 | 7npi.6 | 7npi.7 | 7ojx.1 | 7owd.2 | 7qo4.1 | 7qo5.1 | 7qo6.1 | 7r71.1 | 7uv5.1 | 7uyh.1 | 7w38.1 | 7w39.1 | 7w3a.1 | 7w3b.1 | 7w3c.1 | 7w3f.1 | 7w3g.1 | 7w3h.1 | 7w3i.1 | 7w3j.1 | 7w3k.1 | 7w3m.1 | 7xcr.1 | 7xct.1 | 7xd0.1 | 8b3g.1 | 8b3i.1 | 8c07.1 | 8c83.1 | 8cah.1 | 8cas.1 | 8e7o.1 | 8eaz.1 | 8eaz.2 | 8eb0.1 | 8f1f.1 | 8f1f.2 | 8grm.1 | 8h1t.1 | 8ic9.1 | 8ic9.2 | 8itp.1 | 8itp.2 | 8j1p.1 | 8off.1 | 8pjn.1 | 8pmq.1 | 8rx0.1 | 8svf.1 | 8u5h.1 | 8xep.1 | 9avt.1 | 9d1i.1

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Background

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