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SMTL ID : 1qlf.1

MHC CLASS I H-2DB COMPLEXED WITH GLYCOPEPTIDE K3G

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

hetero-1-1-mer

Ligands

1 x PHE- ALA- PRO- SER- ASN- TYR- PRO- ALA- LEU: SYNTHETIC GLYCOPEPTIDE(Non-covalent)

PHE-ALA-PRO-SER-ASN-TYR-PRO-ALA-LEU.1:

31 residues within 4Å:

Chain A: M.5, Y.7, E.9, Y.45, Y.59, E.63, K.66, Q.70, W.73, V.76, S.77, N.80, L.81, Y.84, L.95, Q.97, S.99, F.116, Y.123, T.143, K.146, W.147, S.150, A.152, H.155, Y.156, Y.159, E.163, W.167, Y.171
Ligands: NAG.5

32 PLIP interactions:

32 interactions with chain A

Hydrophobic interactions: A:Y.7, A:W.73, A:W.73, A:V.76, A:L.81, A:L.95, A:Y.123, A:W.147, A:W.147, A:A.152, A:H.155, A:Y.159, A:E.163, A:W.167, A:W.167
Hydrogen bonds: A:Y.7, A:E.63, A:Q.70, A:Q.70, A:S.77, A:N.80, A:Y.84, A:Q.97, A:Q.97, A:K.146, A:Y.156, A:Y.156, A:Y.171
Salt bridges: A:K.146
pi-Stacking: A:H.155, A:W.167
pi-Cation interactions: A:K.66

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2:	3 residues within 4Å: Chain A: E.166, W.167, R.170 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.167, A:R.170, A:R.170
GOL.4:	5 residues within 4Å: Chain A: F.8, Y.27, N.30 Chain B: F.56, Y.63 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.30, A:N.30, B:F.56 Water bridges: A:N.30, B:Y.63

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

SO4.3:

2 residues within 4Å:

Chain A: R.121
Chain B: I.1

3 PLIP interactions:

2 interactions with chain B, 1 interactions with chain A

Hydrogen bonds: B:I.1, B:I.1
Salt bridges: A:R.121

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG.5:

3 residues within 4Å:

Ligands: PHE-ALA-PRO-SER-ASN-TYR-PRO-ALA-LEU.1, PHE-ALA-PRO-SER-ASN-TYR-PRO-ALA-LEU.1, PHE-ALA-PRO-SER-ASN-TYR-PRO-ALA-LEU.1

No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Glithero, A. et al., Crystal Structures of Two H-2Db/Glycopeptide Complexes Suggest a Molecular Basis for Ctl Cross-Reactivity. Immunity (1999)

Release Date

1999-09-01

Peptides

MHC CLASS I H-2DB HEAVY CHAIN: A
HUMAN BETA-2-MICROGLOBULIN: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

MHC CLASS I H-2DB HEAVY CHAIN

HUMAN BETA-2-MICROGLOBULIN

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1n5a.2 | 1n5a.3 | 1n5a.4 | 1onq.1 | 1onq.2 | 1p7q.1 | 1r3h.1 | 1r3h.2 | 1r3h.3 | 1r3h.4 | 1s8d.1 | 1t1w.1 | 1t1x.1 | 1t1y.1 | 1t1z.1 | 1t20.1 | 1t21.1 | 1t22.1 | 1vgk.1 | 1wbx.1 | 1wby.1 | 1x7q.1 | 1xh3.1 | 1xr8.1 | 1xr9.1 | 1xz0.1 | 1xz0.2 | 1zhb.1 | 1zhb.2 | 1zhb.3 | 1zhb.4 | 1zhk.1 | 1zhl.1 | 1zs8.1 | 1zs8.2 | 1zs8.3 | 1zs8.4 | 1zs8.5 | 1zs8.6 | 1zsd.1 | 1zvs.1 | 1zvs.2 | 2ak4.1 | 2ak4.2 | 2ak4.3 | 2ak4.4 | 2axf.1 | 2axg.1 | 2cii.1 | 2cik.1 | 2f74.1 | 2f74.2 | 2fyy.1 | 2fz3.1 | 2h26.1 | 2h6p.1 | 2hjk.1 | 2hjl.1 | 2hla.1 | 2hn7.1 | 2nw3.1 | 2nx5.1 | 2nx5.2 | 2nx5.3 | 2nx5.4 | 2po6.1 | 2po6.2 | 2rfx.1 | 2xks.1 | 2ypk.1 | 2ypl.1 | 3c9n.1 | 3cc5.1 | 3cc5.2 | 3cch.1 | 3cch.2 | 3cch.3 | 3cch.4 | 3cch.5 | 3cch.6 | 3ch1.1 | 3ch1.2 | 3ch1.3 | 3ch1.4 | 3d2u.1 | 3d2u.2 | 3dbx.1 | 3dx6.1 | 3dx7.1 | 3dx8.1 | 3dxa.1 | 3dxa.2 | 3dxa.3 | 3hla.1 | 3huj.1 | 3huj.2 | 3kpl.1 | 3kpm.1 | 3kpn.1 | 3kpp.1 | 3kpq.1 | 3kpr.1 | 3kpr.2 | 3kps.1 | 3kww.1 | 3kxf.1 | 3kxf.2 | 3kxf.3 | 3kxf.4 | 3l3d.1 | 3l3g.1 | 3l3i.1 | 3l3j.1 | 3l3k.1 | 3ln4.1 | 3ln5.1 | 3m17.2 | 3m17.4 | 3m17.6 | 3m17.8 | 3m1b.2 | 3m1b.4 | 3m1b.6 | 3m1b.8 | 3mv7.1 | 3quk.1 | 3quk.2 | 3qul.1 | 3qul.2 | 3qul.3 | 3qul.4 | 3rew.1 | 3rew.2 | 3rl2.1 | 3sdx.1 | 3sdx.2 | 3spv.1 | 3t8x.1 | 3t8x.2 | 3tbs.1 | 3tbs.2 | 3tbt.1 | 3tbt.2 | 3tbt.3 | 3tbt.4 | 3tbv.1 | 3tbv.2 | 3tbv.3 | 3tbv.4 | 3tbw.1 | 3tbw.2 | 3tbw.3 | 3tbw.4 | 3tby.1 | 3tby.2 | 3tby.3 | 3tby.4 | 3tid.1 | 3tie.1 | 3tie.2 | 3tzv.1 | 3upr.1 | 3upr.2 | 3vcl.1 | 3vfn.1 | 3vfo.1 | 3vfp.1 | 3vfs.1 | 3vfw.1 | 3vh8.1 | 3vh8.2 | 3vwj.1 | 3vwk.1 | 3x11.1 | 3x12.1 | 3x13.1 | 3x14.1 | 4g8i.1 | 4g9d.1 | 4gup.1 | 4gup.2 | 4hwz.1 | 4hx1.1 | 4i48.1 | 4jqv.1 | 4jqx.1 | 4jrx.1 | 4k71.1 | 4k71.2 | 4k71.3 | 4l4t.1 | 4l4t.2 | 4l4v.1 | 4l4v.2 | 4lcw.1 | 4lcw.2 | 4lnr.1 | 4mji.1 | 4mji.2 | 4n0f.1 | 4n0f.2 | 4n0f.3 | 4n0f.4 | 4n0u.1 | 4nnx.1 | 4nny.1 | 4no0.1 | 4no2.1 | 4no3.1 | 4nqc.1 | 4nqc.2 | 4nqd.1 | 4nqd.2 | 4nqd.5 | 4nqe.1 | 4nqe.2 | 4nsk.1 | 4o2c.1 | 4o2e.1 | 4o2e.2 | 4o2f.1 | 4o2f.2 | 4pj7.1 | 4pj7.2 | 4pj8.1 | 4pr5.1 | 4pra.1 | 4prb.1 | 4prd.1 | 4pre.1 | 4pri.1 | 4prn.1 | 4prp.1 | 4qrr.1 | 4qru.1 | 4uq2.1 | 4uq2.2 | 4wu7.1 | 4wu7.2 | 4ww2.1 | 4x6d.1 | 4x6d.2 | 5b38.1 | 5b39.1 | 5bjt.1 | 5bjt.2 | 5bjt.3 | 5bjt.4 | 5ddh.1 | 5e8n.1 | 5e8n.2 | 5e8n.3 | 5e8n.4 | 5e8o.1 | 5e8o.2 | 5e8p.1 | 5e8p.2 | 5enw.1 | 5f1i.1 | 5f1i.2 | 5f1i.3 | 5f1i.4 | 5f1i.5 | 5f1i.6 | 5f1i.7 | 5f1i.8 | 5f7d.1 | 5fa3.1 | 5gr7.1 | 5grd.1 | 5grg.1 | 5gsb.1 | 5gsd.1 | 5gsv.1 | 5gsx.1 | 5gsx.2 | 5im7.1 | 5im7.2 | 5inc.1 | 5inc.2 | 5ind.1 | 5ind.2 | 5jwe.1 | 5jwe.2 | 5jwe.3 | 5jwe.4 | 5m00.1 | 5m01.1 | 5m02.1 | 5mzm.1 | 5mzm.2 | 5nmh.1 | 5opi.1 | 5swq.1 | 5t6w.1 | 5t6x.1 | 5t6y.1 | 5t6z.1 | 5t70.1 | 5til.1 | 5til.2 | 5tje.1 | 5tje.2 | 5u16.1 | 5u16.2 | 5u17.1 | 5u17.2 | 5u2v.1 | 5u2v.2 | 5u6q.1 | 5u6q.2 | 5u72.1 | 5u72.2 | 5u98.1 | 5u98.2 | 5v5m.1 | 5v5m.2 | 5vud.1 | 5vue.1 | 5vuf.1 | 5vvp.1 | 5vwd.1 | 5vwf.1 | 5vwj.1 | 5wke.1 | 5wkg.1 | 5wki.1 | 5wl1.1 | 5wwj.1 | 5wwj.2 | 5wwu.1 | 5xos.1 | 5xot.1 | 6avf.1 | 6bj2.1 | 6bj3.1 | 6bj8.1 | 6bxp.1 | 6c97.1 | 6c97.2 | 6c98.1 | 6c98.2 | 6c99.1 | 6c99.2 | 6cug.1 | 6eny.1 | 6ewa.1 | 6ewa.2 | 6ewc.1 | 6ewc.2 | 6ewo.1 | 6ewo.2 | 6fgb.1 | 6g9q.1 | 6g9r.1 | 6g9r.2 | 6g9r.3 | 6g9r.4 | 6ilm.1 | 6ilm.2 | 6ilm.3 | 6ilm.4 | 6j1v.1 | 6j1w.1 | 6j29.1 | 6j2a.1 | 6j2e.1 | 6j2e.2 | 6j2g.1 | 6j2g.2 | 6j2i.1 | 6j2i.2 | 6j2j.1 | 6j2j.2 | 6joz.1 | 6jp3.1 | 6k7t.1 | 6la6.1 | 6la6.2 | 6la6.3 | 6la6.4 | 6la7.1 | 6la7.2 | 6la7.3 | 6la7.4 | 6mtl.1 | 6mtm.1 | 6mwr.1 | 6nha.1 | 6o4y.1 | 6o4z.1 | 6o51.1 | 6o53.1 | 6p23.1 | 6p27.1 | 6p2c.1 | 6pbh.1 | 6pyj.1 | 6pyv.1 | 6pz5.1 | 6uln.1 | 6ulr.1 | 6uon.1 | 6uon.2 | 6vb1.1 | 6vb6.1 | 6vqy.1 | 6vqy.2 | 6vqz.1 | 6vqz.2 | 6wna.1 | 6wol.1 | 6wzy.1 | 7b5f.1 | 7c9v.1 | 7c9v.2 | 7c9v.3 | 7c9v.4 | 7edo.2 | 7kgo.1 | 7kgp.1 | 7kgq.1 | 7kgr.1 | 7kgs.1 | 7kgt.1 | 7p0a.1 | 7p0a.2 | 7p0t.1 | 7p0t.2 | 7qpd.1 | 7sif.1 | 7sih.1 | 7t0l.1 | 7t0l.2 | 7t5m.1 | 7t5m.2 | 7wkj.1 | 7wzz.1 | 7x00.1 | 7x1b.1 | 7x1c.1 | 7xf3.1 | 7yg3.1 | 8dv4.1 | 8ec5.1 | 8elg.1 | 8elh.1 | 8erx.1 | 8esh.1 | 8f5a.1 | 8f7m.1 | 8i5c.1 | 8i5c.2 | 8i5c.3 | 8i5c.4 | 8i5c.5 | 8i5c.6 | 8i5c.7 | 8i5c.8 | 8i5c.9 | 8i5c.10 | 8i5d.1 | 8i5e.1 | 8isn.1 | 8isn.2 | 8tub.1 | 8tub.2 | 8tub.3 | 8tub.4 | 8udr.1 | 8vra.1 | 8wte.1 | 8wte.2 | 8wul.1 | 8wul.2 | 8wul.3 | 8wul.4 | 8xes.1 | 8xfz.1 | 8xg2.1 | 8xkc.1 | 8ye4.1 | 8ye4.2

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