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SMTL ID : 6v80.2 (1 other biounit)

Crystal structure of human CD1d presenting alpha-Galactosylceramide in complex with NKT12 TCR and VHH nanobody 1D12

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.53 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1:

3 residues within 4Å:

Chain A: T.21, R.22, N.39

1 PLIP interactions:

1 interactions with chain A

Hydrogen bonds: A:K.79

1 x AGH: N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE(Non-covalent)

AGH.2:

25 residues within 4Å:

Chain A: C.9, L.10, Q.11, L.26, A.27, V.44, L.63, F.67, Y.70, S.73, F.74, D.77, V.78, F.81, F.111, D.148, W.150, T.151, L.158
Chain C: F.32, S.33, F.54, D.96, R.97, G.98

19 PLIP interactions:

4 interactions with chain C, 15 interactions with chain A

Hydrogen bonds: C:F.32, C:F.32, C:R.97, C:G.98, A:S.73, A:T.151, A:T.151
Hydrophobic interactions: A:Q.11, A:A.27, A:V.44, A:L.63, A:F.67, A:F.74, A:F.74, A:V.78, A:F.81, A:F.111, A:T.151, A:L.158

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

NAG.3:	1 residues within 4Å: Chain A: N.160 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.160
NAG.4:	2 residues within 4Å: Chain A: N.17, S.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.19, A:S.19

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Shahine, A. et al., A single-domain bispecific antibody targeting CD1d and the NKT T-cell receptor induces a potent antitumor response. Nat Cancer (2020)

Release Date

2020-09-16

Peptides

Antigen-presenting glycoprotein CD1d: A
Beta-2-microglobulin: B
T cell receptor alpha variable 10, nkt tcr alpha chain fusion: C
nkt tcr beta chain: D
Nanobody VHH ID12: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
G

C
H

D
I

E
J

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Antigen-presenting glycoprotein CD1d

Beta-2-microglobulin

T cell receptor alpha variable 10, nkt tcr alpha chain fusion

nkt tcr beta chain

Nanobody VHH ID12

Related Entries With Identical Sequence

1a9b.1 | 1a9b.2 | 1a9e.1 | 1b0g.1 | 1b0g.2 | 1b0r.1 | 1bd2.1 | 1cg9.1 | 1duy.1 | 1duy.2 | 1duz.1 | 1duz.2 | 1eey.1 | 1eey.2 | 1eez.1 | 1eez.2 | 1efx.1 | 1gzp.1 | 1gzq.1 | 1hhg.1 | 1hhg.2 | 1hhh.1 | 1hhi.1 | 1hhi.2 | 1hhj.1 | 1hhj.2 | 1hhk.1 | 1hhk.2 | 1i1f.1 | 1i1f.2 more...less...

1i1y.1 | 1i1y.2 | 1i4f.1 | 1i7r.1 | 1i7r.2 | 1i7t.1 | 1i7t.2 | 1i7u.1 | 1i7u.2 | 1im3.1 | 1im3.2 | 1im3.3 | 1im3.4 | 1im9.1 | 1jf1.1 | 1jgd.1 | 1jge.1 | 1jht.1 | 1jnj.1 | 1k5n.1 | 1kpr.1 | 1kpr.2 | 1kpr.3 | 1kpr.4 | 1ktl.1 | 1ktl.2 | 1ktl.3 | 1lds.1 | 1lp9.1 | 1lp9.2 | 1mhe.1 | 1of2.1 | 1oga.1 | 1ogt.1 | 1q94.1 | 1q94.2 | 1qew.1 | 1qr1.1 | 1qr1.2 | 1qrn.1 | 1qse.1 | 1qsf.1 | 1qvo.1 | 1qvo.2 | 1s9w.1 | 1s9x.1 | 1s9y.1 | 1sys.1 | 1syv.1 | 1tmc.1 | 1tvb.1 | 1tvb.2 | 1tvh.1 | 1tvh.2 | 1uqs.1 | 1uxs.1 | 1uxw.1 | 1w0v.1 | 1w0w.1 | 1w72.1 | 1w72.2 | 1ydp.1 | 1ydp.2 | 1zt4.1 | 1zt4.2 | 1zt4.3 | 2a83.1 | 2av1.1 | 2av1.2 | 2av7.1 | 2av7.2 | 2bck.1 | 2bck.2 | 2bck.3 | 2bnq.1 | 2bnr.1 | 2bsr.1 | 2bss.1 | 2bst.1 | 2bvo.1 | 2bvp.1 | 2bvq.1 | 2c7u.1 | 2c7u.2 | 2clr.1 | 2clr.2 | 2d31.1 | 2d31.2 | 2d4f.1 | 2dyp.1 | 2esv.1 | 2eyr.1 | 2eyr.2 | 2eys.1 | 2eys.2 | 2eyt.1 | 2eyt.2 | 2eyt.3 | 2f74.1 | 2f74.2 | 2git.1 | 2git.2 | 2gj6.1 | 2gt9.1 | 2gt9.2 | 2gtw.1 | 2gtw.2 | 2gtz.1 | 2gtz.2 | 2guo.1 | 2guo.2 | 2j8u.1 | 2j8u.2 | 2jcc.1 | 2jcc.2 | 2uwe.1 | 2uwe.2 | 2v2w.1 | 2v2w.2 | 2v2x.1 | 2v2x.2 | 2vlj.1 | 2vlk.1 | 2vll.1 | 2vll.2 | 2vlr.1 | 2vlr.2 | 2x4n.1 | 2x4n.2 | 2x4o.1 | 2x4o.2 | 2x4p.1 | 2x4p.2 | 2x4q.1 | 2x4q.2 | 2x4r.1 | 2x4r.2 | 2x4s.1 | 2x4s.2 | 2x4t.1 | 2x4t.2 | 2x4u.1 | 2x4u.2 | 2x70.1 | 2x70.2 | 2yxf.1 | 3am8.1 | 3am8.2 | 3b3i.1 | 3b6s.1 | 3bgm.1 | 3bh8.1 | 3bh9.1 | 3bh9.2 | 3bo8.1 | 3bp4.1 | 3bp7.1 | 3bvn.1 | 3bvn.2 | 3bw9.1 | 3bwa.1 | 3bxn.1 | 3bze.1 | 3bze.2 | 3bze.3 | 3bze.4 | 3cdg.1 | 3cdg.2 | 3cii.1 | 3cii.2 | 3czf.1 | 3d18.1 | 3d39.1 | 3d3v.1 | 3dtx.1 | 3dtx.2 | 3ffc.1 | 3ffc.2 | 3ft2.1 | 3ft3.1 | 3ft4.1 | 3giv.1 | 3giv.2 | 3gjf.1 | 3gjf.2 | 3gsn.1 | 3gso.1 | 3gsq.1 | 3gsr.1 | 3gsu.1 | 3gsv.1 | 3gsw.1 | 3gsx.1 | 3h7b.1 | 3h7b.2 | 3h9h.1 | 3h9h.2 | 3h9s.1 | 3hae.1 | 3hae.2 | 3hae.3 | 3hae.4 | 3hcv.1 | 3hg1.1 | 3hpj.1 | 3hpj.2 | 3i6g.1 | 3i6g.2 | 3i6k.1 | 3i6k.2 | 3i6l.1 | 3ixa.1 | 3ixa.2 | 3kla.1 | 3kla.2 | 3kpo.1 | 3kyn.1 | 3kyo.1 | 3kyo.2 | 3lkn.1 | 3lko.1 | 3lkp.1 | 3lkq.1 | 3lkr.1 | 3lks.1 | 3low.1 | 3lv3.1 | 3mgo.1 | 3mgo.2 | 3mgo.3 | 3mgo.4 | 3mgt.1 | 3mgt.2 | 3mgt.3 | 3mgt.4 | 3mr9.1 | 3mrb.1 | 3mrc.1 | 3mrd.1 | 3mre.1 | 3mrf.1 | 3mrg.1 | 3mrh.1 | 3mri.1 | 3mrj.1 | 3mrk.1 | 3mrl.1 | 3mrm.1 | 3mrn.1 | 3mro.1 | 3mrp.1 | 3mrq.1 | 3mrr.1 | 3mv8.1 | 3mv9.1 | 3myj.1 | 3myj.2 | 3nfn.1 | 3o3a.1 | 3o3a.2 | 3o3b.1 | 3o3b.2 | 3o3d.1 | 3o3d.2 | 3o3e.1 | 3o3e.2 | 3ox8.1 | 3ox8.2 | 3oxr.1 | 3oxs.1 | 3pwj.1 | 3pwj.2 | 3pwl.1 | 3pwl.2 | 3pwn.1 | 3pwn.2 | 3pwp.1 | 3qdg.1 | 3qdj.1 | 3qdm.1 | 3qeq.1 | 3qfd.1 | 3qfd.2 | 3qfj.1 | 3qzw.1 | 3qzw.2 | 3rl1.1 | 3rwj.1 | 3sjv.1 | 3sjv.2 | 3sjv.3 | 3sjv.4 | 3skm.1 | 3sko.1 | 3to2.1 | 3utq.1 | 3uts.1 | 3uts.2 | 3utt.1 | 3utt.2 | 3v5d.1 | 3v5d.2 | 3v5h.1 | 3v5h.2 | 3v5k.1 | 3v5k.2 | 3vfm.1 | 3vfr.1 | 3vft.1 | 3vfu.1 | 3vfv.1 | 3vri.1 | 3vrj.1 | 3vxm.1 | 3vxn.1 | 3vxo.1 | 3vxo.2 | 3vxp.1 | 3vxp.2 | 3vxr.1 | 3vxs.1 | 3vxu.1 | 3vxu.2 | 3w0w.1 | 3w39.1 | 3w39.2 | 3wl9.1 | 3wlb.1 | 4e5x.1 | 4e5x.2 | 4eup.1 | 4eup.2 | 4f7m.1 | 4f7m.2 | 4f7p.1 | 4f7t.1 | 4f7t.2 | 4ftv.1 | 4g8g.1 | 4g9f.1 | 4gkn.1 | 4gkn.2 | 4gks.1 | 4gks.2 | 4hkj.1 | 4hkj.2 | 4hkj.3 | 4hkj.4 | 4i4w.1 | 4jfd.1 | 4jfe.1 | 4jff.1 | 4jfo.1 | 4jfo.2 | 4jfp.1 | 4jfp.2 | 4jfq.1 | 4jfq.2 | 4jry.1 | 4k7f.1 | 4k7f.2 | 4l29.1 | 4l29.2 | 4l29.3 | 4l29.4 | 4l29.5 | 4l29.6 | 4l29.7 | 4l29.8 | 4l29.9 | 4l29.10 | 4l29.11 | 4l29.12 | 4l29.13 | 4l29.14 | 4l3e.1 | 4lcy.2 | 4lcy.4 | 4lcy.5 | 4lcy.6 | 4lhu.1 | 4mj5.1 | 4mj6.1 | 4mnq.1 | 4n8v.1 | 4n8v.2 | 4nqv.1 | 4nqv.2 | 4nqv.3 | 4nqv.4 | 4nqv.5 | 4nqv.6 | 4nqx.1 | 4nqx.2 | 4nqx.3 | 4nqx.4 | 4nqx.5 | 4nqx.6 | 4pj5.1 | 4pj5.2 | 4pj9.1 | 4pja.1 | 4pja.2 | 4pjb.1 | 4pjb.2 | 4pjc.1 | 4pjc.2 | 4pjd.1 | 4pjd.2 | 4pje.1 | 4pje.2 | 4pjf.1 | 4pjf.2 | 4pjg.1 | 4pjg.2 | 4pjh.1 | 4pjh.2 | 4pji.1 | 4pji.2 | 4pjx.1 | 4pjx.2 | 4qok.1 | 4qrp.1 | 4qrp.2 | 4qrp.4 | 4qrq.1 | 4qrt.1 | 4u1h.1 | 4u1i.1 | 4u1j.1 | 4u1k.1 | 4u1k.2 | 4u1l.1 | 4u1l.2 | 4u1m.1 | 4u1n.1 | 4u1s.1 | 4u6x.1 | 4u6y.1 | 4uq3.1 | 4uq3.2 | 4wdi.1 | 4wdi.2 | 4wj5.1 | 4wj5.2 | 4wo4.1 | 4wu5.1 | 4wu5.2 | 4wuu.1 | 4xxc.1 | 4z76.1 | 4z76.2 | 4z77.1 | 4z77.2 | 4z78.1 | 4z78.2 | 4z78.3 | 5brz.1 | 5bs0.1 | 5c07.1 | 5c07.2 | 5c08.1 | 5c08.2 | 5c09.1 | 5c09.2 | 5c0a.1 | 5c0a.2 | 5c0b.1 | 5c0b.2 | 5c0c.1 | 5c0c.2 | 5c0d.1 | 5c0e.1 | 5c0f.1 | 5c0g.1 | 5c0i.1 | 5c0j.1 | 5cs7.1 | 5d2l.1 | 5d2l.2 | 5d2l.3 | 5d2l.4 | 5d2n.1 | 5d2n.2 | 5d5m.1 | 5d5m.2 | 5d7i.1 | 5d7i.2 | 5d7j.1 | 5d7j.2 | 5d7l.1 | 5d7l.2 | 5d9s.1 | 5def.1 | 5deg.1 | 5e00.1 | 5e6i.1 | 5e6i.2 | 5e6i.3 | 5e6i.4 | 5e9d.1 | 5e9d.2 | 5eo0.1 | 5eo1.1 | 5eot.1 | 5eu3.1 | 5eu4.1 | 5eu4.2 | 5eu5.1 | 5eu6.1 | 5euo.1 | 5euo.2 | 5fa4.1 | 5fdw.1 | 5hga.1 | 5hga.2 | 5hgb.1 | 5hgb.2 | 5hgb.3 | 5hgb.4 | 5hgd.1 | 5hgd.2 | 5hgh.1 | 5hhm.1 | 5hhm.2 | 5hhn.1 | 5hho.1 | 5hhp.1 | 5hhq.1 | 5hyj.1 | 5hyj.2 | 5ib1.1 | 5ib2.1 | 5ib3.1 | 5ib4.1 | 5ib5.1 | 5ib5.2 | 5ieh.1 | 5iek.1 | 5iro.1 | 5iro.2 | 5iro.3 | 5iro.4 | 5iro.5 | 5iro.6 | 5jhd.1 | 5jhd.2 | 5jzi.1 | 5jzi.2 | 5men.1 | 5meo.1 | 5mep.1 | 5mep.2 | 5meq.1 | 5mer.1 | 5mer.2 | 5n1y.1 | 5n6b.1 | 5n6b.2 | 5nht.1 | 5nme.1 | 5nme.2 | 5nmf.1 | 5nmf.2 | 5nmg.1 | 5nmg.2 | 5nmk.1 | 5nq1.1 | 5nq1.2 | 5nq3.1 | 5nq3.2 | 5nqk.1 | 5trz.1 | 5ts1.1 | 5ts1.2 | 5ts1.3 | 5ts1.4 | 5txs.1 | 5u1r.1 | 5u1r.2 | 5v5l.1 | 5v5l.2 | 5vgd.1 | 5vge.1 | 5vwh.1 | 5vz5.1 | 5w1v.1 | 5w1v.2 | 5w1v.3 | 5w1v.4 | 5w1w.1 | 5w1w.2 | 5w1w.3 | 5w1w.4 | 5w67.1 | 5w69.1 | 5w69.2 | 5w69.3 | 5w69.4 | 5w6a.1 | 5w6a.2 | 5wer.1 | 5wer.2 | 5wer.3 | 5wer.4 | 5wjl.1 | 5wjl.2 | 5wjl.3 | 5wjn.1 | 5wjn.2 | 5wjn.3 | 5wkf.1 | 5wkf.2 | 5wkh.1 | 5wkh.2 | 5wmn.1 | 5wmn.2 | 5wmq.1 | 5wmr.1 | 5wsh.1 | 5xov.1 | 5xov.2 | 6aee.1 | 6aee.2 | 6am5.1 | 6amt.1 | 6amt.2 | 6amu.1 | 6at9.1 | 6bxq.1 | 6d29.1 | 6d2b.1 | 6d2r.1 | 6d2t.1 | 6d78.1 | 6dkp.1 | 6ei2.1 | 6eqa.1 | 6eqb.1 | 6g3j.1 | 6g3j.2 | 6g3k.1 | 6g3k.2 | 6ggm.1 | 6ggm.2 | 6gh1.1 | 6gh1.2 | 6gh1.3 | 6gh1.4 | 6gh4.1 | 6gh4.2 | 6gh4.3 | 6gh4.4 | 6ghn.1 | 6ghn.2 | 6gl1.1 | 6gl1.2 | 6gl1.3 | 6gl1.4 | 6id4.1 | 6id4.2 | 6iex.1 | 6k60.1 | 6k60.2 | 6m24.1 | 6m2j.1 | 6m2k.1 | 6mpp.1 | 6mt3.1 | 6mt4.1 | 6mt5.1 | 6mt6.1 | 6nca.1 | 6nca.2 | 6nca.3 | 6nca.4 | 6nca.5 | 6nca.6 | 6nca.7 | 6nca.8 | 6nca.9 | 6nca.10 | 6nca.11 | 6nca.12 | 6nca.13 | 6nca.14 | 6nca.15 | 6nca.16 | 6nca.17 | 6nca.18 | 6nca.19 | 6nca.20 | 6npr.1 | 6npr.2 | 6opd.1 | 6p2f.1 | 6p2s.1 | 6p64.1 | 6p64.2 | 6pa1.1 | 6pa1.2 | 6pag.1 | 6ptb.1 | 6ptb.2 | 6pte.1 | 6pte.2 | 6pte.3 | 6pte.4 | 6puc.1 | 6puc.2 | 6pud.1 | 6pud.2 | 6pue.1 | 6pue.2 | 6puf.1 | 6puf.2 | 6pug.1 | 6pug.2 | 6puh.1 | 6puh.2 | 6pui.1 | 6pui.2 | 6puj.1 | 6puj.2 | 6puk.1 | 6puk.2 | 6pul.1 | 6pul.2 | 6pum.1 | 6pum.2 | 6pvc.1 | 6pvc.2 | 6pvd.1 | 6pvd.2 | 6pyl.1 | 6pyw.1 | 6q3k.1 | 6q3s.1 | 6r2l.1 | 6rp9.1 | 6rp9.2 | 6rpa.1 | 6rpb.1 | 6rpb.2 | 6rpb.3 | 6rpb.4 | 6rsy.1 | 6rsy.2 | 6ss7.1 | 6ss7.2 | 6ss8.1 | 6ss8.2 | 6ss9.1 | 6ss9.2 | 6ssa.1 | 6ssa.2 | 6ssa.3 | 6ssa.4 | 6tdo.1 | 6tdp.1 | 6tdq.1 | 6tdq.2 | 6tdr.1 | 6tdr.2 | 6tds.1 | 6tds.2 | 6tmo.1 | 6trn.1 | 6tro.1 | 6ujo.1 | 6ujq.1 | 6uk2.1 | 6uk4.1 | 6uli.1 | 6ulk.1 | 6uz1.1 | 6uz1.2 | 6uzm.1 | 6uzn.1 | 6uzo.1 | 6uzp.1 | 6uzq.1 | 6uzs.1 | 6v2o.1 | 6v2p.1 | 6v2q.1 | 6v3j.1 | 6v7y.1 | 6v7z.1 | 6v7z.2 | 6v80.1 | 6vb0.1 | 6vb3.1 | 6vb7.1 | 6viu.1 | 6vm7.1 | 6vm8.1 | 6vm9.1 | 6vma.1 | 6vmc.1 | 6vmx.1 | 6vmx.2 | 6vpz.1 | 6vq2.1 | 6vqd.1 | 6vqe.1 | 6vqo.1 | 6vqo.2 | 6vr1.1 | 6vr1.2 | 6vr5.1 | 6vr5.2 | 6vrm.1 | 6vrn.1 | 6w9u.1 | 6w9u.2 | 6w9v.1 | 6w9v.2 | 6x00.1 | 6xqa.1 | 6xqa.2 | 6xqp.1 | 6xqp.2 | 6y26.1 | 6y27.1 | 6y28.1 | 6y29.1 | 6y2a.1 | 6y2b.1 | 6z9v.1 | 6z9v.2 | 6z9w.1 | 6z9w.2 | 6z9x.1 | 6z9x.2 | 6zkw.1 | 6zkx.1 | 6zky.1 | 6zkz.1 | 7alo.1 | 7alo.2 | 7bbg.1 | 7bh8.1 | 7ciq.1 | 7cir.1 | 7cis.1 | 7duu.1 | 7dyn.1 | 7dzm.1 | 7dzn.1 | 7edo.1 | 7jwi.1 | 7jyu.1 | 7jyu.2 | 7jyv.1 | 7jyw.1 | 7jyx.1 | 7jyx.2 | 7k80.1 | 7k80.2 | 7k81.1 | 7l1b.1 | 7l1c.1 | 7l1d.1 | 7lfz.1 | 7lg0.1 | 7lg2.1 | 7lg3.1 | 7lgd.1 | 7lgd.2 | 7lgt.1 | 7lgt.2 | 7lli.1 | 7lli.2 | 7llj.1 | 7llj.2 | 7m8s.1 | 7m8s.2 | 7m8t.1 | 7m8u.1 | 7mj6.1 | 7mj7.1 | 7mj8.1 | 7mj9.1 | 7mja.1 | 7mkb.1 | 7mle.1 | 7n1a.1 | 7n1a.2 | 7n1b.1 | 7n1b.2 | 7n1e.1 | 7n1f.1 | 7n6d.1 | 7n6d.2 | 7n6d.3 | 7n6d.4 | 7n6e.1 | 7n6e.2 | 7ndq.1 | 7ndt.1 | 7ndu.1 | 7nui.1 | 7p3d.1 | 7p3e.1 | 7p3e.2 | 7pbe.1 | 7pbe.2 | 7rm4.1 | 7rm4.2 | 7rm4.3 | 7rm4.4 | 7rrg.1 | 7rtd.1 | 7rtr.1 | 7s8q.1 | 7s8q.2 | 7s8r.1 | 7s8r.2 | 7s8s.1

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