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SMTL ID : 7x00.1

Crystal structure of peptide VSFIEFVGW in complex with HLA-B5801

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

hetero-1-1-mer

Ligands

1 x VAL- SER- PHE- ILE- GLU- PHE- VAL- GLY- TRP: VAL-SER-PHE-ILE-GLU-PHE-VAL-GLY-TRP(Non-covalent)

VAL-SER-PHE-ILE-GLU-PHE-VAL-GLY-TRP.1:

26 residues within 4Å:

Chain A: Y.7, Y.9, Y.59, E.63, N.66, M.67, S.70, T.73, Y.74, N.77, I.80, Y.84, I.95, R.97, Y.99, A.117, Y.123, T.143, K.146, W.147, V.152, Q.155, L.156, Y.159, W.167, Y.171

32 PLIP interactions:

32 interactions with chain A

Hydrophobic interactions: A:Y.59, A:N.77, A:I.95, A:I.95, A:I.95, A:Y.99, A:Q.155, A:Q.155, A:L.156, A:Y.159, A:W.167, A:W.167
Hydrogen bonds: A:Y.7, A:E.63, A:N.66, A:N.77, A:Y.99, A:Y.99, A:Y.159, A:Y.171
Water bridges: A:N.66, A:S.70, A:S.70, A:S.70, A:Y.74, A:Y.74, A:N.77, A:N.77, A:S.116, A:K.146
Salt bridges: A:R.97
pi-Stacking: A:Y.123

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2:

6 residues within 4Å:

Chain A: R.6, F.8, Y.27, D.29, D.30
Chain B: Y.63

3 PLIP interactions:

2 interactions with chain B, 1 interactions with chain A

Water bridges: B:F.56, B:Y.63
Hydrogen bonds: A:D.30

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Huan, X. et al., Allopurinol non-covalently facilitates binding of unconventional peptides to HLA-B*58:01. Sci Rep (2023)

Release Date

2023-05-03

Peptides

MHC class I antigen: A
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 antigen

Beta-2-microglobulin

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1a1m.1 | 1a1n.1 | 1a1o.1 | 1a6z.1 | 1a6z.2 | 1agb.1 | 1agc.1 | 1agd.1 | 1age.1 | 1agf.1 | 1akj.1 | 1c16.1 | 1c16.2 | 1c16.3 | 1c16.4 | 1c16.5 | 1de4.1 | 1de4.2 | 1e27.1 | 1e28.1 | 1exu.1 | 1hsa.1 | 1hsa.2 | 1hsb.1 | 1m05.1 | 1m05.2 | 1m6o.1 | 1mi5.1 | 1n2r.1 | 1onq.1 more...less...

1onq.2 | 1p7q.1 | 1qlf.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 | 1x7q.1 | 1xh3.1 | 1xr8.1 | 1xr9.1 | 1xz0.1 | 1xz0.2 | 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 | 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 | 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 | 3rew.1 | 3rew.2 | 3rl2.1 | 3sdx.1 | 3sdx.2 | 3spv.1 | 3t8x.1 | 3t8x.2 | 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 | 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 | 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 | 5nmh.1 | 5opi.1 | 5swq.1 | 5t6w.1 | 5t6x.1 | 5t6y.1 | 5t6z.1 | 5t70.1 | 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 | 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 | 7qpd.1 | 7sif.1 | 7sih.1 | 7t0l.1 | 7t0l.2 | 7t5m.1 | 7t5m.2 | 7wkj.1 | 7wzz.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 | 8vjz.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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Background

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