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SMTL ID : 7re7.2 (1 other biounit)

TCR mimic antibody (Fab fragment) in complex with AFP/HLA-A*02

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x PHE- MET- ASN- LYS- PHE- ILE- TYR- GLU- ILE: PHE-MET-ASN-LYS-PHE-ILE-TYR-GLU-ILE(Non-covalent)

PHE-MET-ASN-LYS-PHE-ILE-TYR-GLU-ILE.1:

41 residues within 4Å:

Chain A: P.30, N.31, Y.32, W.33, R.50, D.52
Chain B: Y.32, Y.93, T.95, G.96, S.97, R.98
Chain C: M.5, Y.7, F.9, M.45, E.63, K.66, V.67, H.70, T.73, V.76, D.77, T.80, L.81, Y.84, R.97, Y.99, Y.116, Y.123, T.143, K.146, W.147, A.150, V.152, Q.155, L.156, Y.159, T.163, W.167, Y.171

37 PLIP interactions:

27 interactions with chain C, 3 interactions with chain A, 7 interactions with chain B

Hydrophobic interactions: C:T.73, C:D.77, C:L.81, C:Y.116, C:Y.123, C:T.143, C:K.146, C:W.147, C:A.150, C:V.152, C:Q.155, C:Y.159, C:T.163, C:W.167, A:P.30, A:W.33
Hydrogen bonds: C:Y.7, C:E.63, C:D.77, C:Y.84, C:Y.99, C:Y.99, C:Y.171, C:Y.171, A:D.52, B:Y.32, B:T.95, B:T.95, B:G.96, B:S.97, B:R.98, B:R.98
Water bridges: C:R.97
Salt bridges: C:K.146
pi-Stacking: C:W.167, C:W.167
pi-Cation interactions: C:K.66

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2:	7 residues within 4Å: Chain A: R.98, Y.100, L.103, D.105 Chain B: Y.51 Chain C: E.58, R.65 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.98
EPE.9:	7 residues within 4Å: Chain C: R.21, I.23 Chain D: S.34, D.35, H.52, L.65, Y.67 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Water bridges: C:R.21 Salt bridges: C:R.21, D:H.52 Hydrogen bonds: D:D.35

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3:	2 residues within 4Å: Chain A: N.159, A.162 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.159
GOL.4:	3 residues within 4Å: Chain A: T.19, S.71, H.82 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.19, A:T.19, A:H.82
GOL.5:	5 residues within 4Å: Chain C: Q.54, E.55, R.170, N.174 Ligands: PG4.6 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.54, C:N.174

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6:	7 residues within 4Å: Chain A: Y.27, F.29 Chain C: E.166, W.167, R.170, E.173 Ligands: GOL.5 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.170, C:R.170, A:Y.27
PG4.7:	5 residues within 4Å: Chain C: Y.85, Q.87, Y.118, K.121 Chain D: I.2 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.87, C:K.121

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.8:

9 residues within 4Å:

Chain C: R.6, F.8, M.98, Y.113, Q.115
Chain D: F.57, S.58, K.59, W.61

1 PLIP interactions:

1 interactions with chain D

Hydrogen bonds: D:K.59

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.10:

5 residues within 4Å:

Chain D: P.6, I.8, L.88, K.92, V.94

2 PLIP interactions:

2 interactions with chain D

Hydrogen bonds: D:I.8, D:K.92

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Liu, C. et al., Validation and promise of a TCR mimic antibody for cancer immunotherapy of hepatocellular carcinoma. Sci Rep (2022)

Release Date

2022-07-27

Peptides

Fab heavy chain: A
Fab light chain: B
MHC class I antigen: C
Beta-2-microglobulin: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

D
B

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Fab heavy chain

Fab light chain

MHC class I antigen

Beta-2-microglobulin

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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 | 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 | 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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 | 6v80.2 | 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 | 7n2n.1 | 7n2o.1 | 7n2p.1 | 7n2q.1 | 7n2q.2 | 7n2r.1 | 7n2s.1 | 7n4k.1 | 7n5c.1 | 7n5p.1 | 7n5q.1 | 7n5q.2 | 7n6d.1 | 7n6d.2 | 7n6d.3 | 7n6d.4 | 7n6e.1 | 7n6e.2 | 7n9j.1 | 7na5.1 | 7ndq.1 | 7ndt.1 | 7ndu.1 | 7nmd.1 | 7nmd.2 | 7nme.1 | 7nmf.1 | 7nmg.1 | 7nui.1 | 7ow3.1 | 7ow3.2 | 7ow3.3 | 7ow3.4 | 7ow4.1 | 7ow4.2 | 7ow4.3 | 7ow4.4 | 7ow5.1 | 7ow6.1 | 7p3d.1 | 7p3e.1 | 7p3e.2 | 7p49.1 | 7p49.2 | 7p49.3 | 7p49.4 | 7p4b.1 | 7p4b.2 | 7p4b.3 | 7p4b.4 | 7pb2.1 | 7pb2.2 | 7pbc.1 | 7pbe.1 | 7pbe.2 | 7pdw.1 | 7pdw.2 | 7q98.1 | 7q98.2 | 7q98.3 | 7q98.4 | 7q98.5 | 7q99.1 | 7q9a.1 | 7q9b.1 | 7qng.1 | 7qpj.1 | 7r7v.1 | 7r7w.1 | 7r7x.1 | 7r7x.2 | 7r80.1 | 7re7.1 | 7re8.1 | 7re8.2 | 7re9.1 | 7re9.2 | 7rk7.1 | 7rm4.1 | 7rm4.2 | 7rm4.3 | 7rm4.4 | 7rrg.1 | 7rtd.1 | 7rtr.1 | 7rzd.1 | 7rzj.1 | 7s79.1 | 7s7d.1 | 7s7e.1 | 7s7f.1 | 7s8a.1 | 7s8e.1 | 7s8f.1 | 7s8q.1 | 7s8q.2 | 7s8r.1 | 7s8r.2 | 7s8s.1 | 7sa2.1 | 7sig.1 | 7sis.1 | 7su9.1 | 7tlt.1 | 7tlt.2 | 7tuc.1 | 7tud.1 | 7tue.1 | 7u1r.1 | 7u21.1 | 7u21.2 | 7uc5.1 | 7uc5.2 | 7ufj.1 | 7ufj.2 | 7um2.1 | 7umg.1 | 7ur1.1 | 7zt2.1 | 7zt3.1 | 7zt4.1 | 7zt5.1 | 7zt7.1 | 7zt8.1 | 7zt9.1 | 7zuc.1 | 7zuc.2 | 8cx4.1 | 8dnt.1 | 8dnt.2 | 8dnt.3 | 8dnt.4 | 8e13.1 | 8e2z.1 | 8e8i.1 | 8eb2.1 | 8eb2.2 | 8eb2.3 | 8ek5.1 | 8emf.1 | 8emg.1 | 8emi.1 | 8emj.1 | 8emk.1 | 8en8.1 | 8en8.2 | 8enh.1 | 8enh.2 | 8enh.3 | 8enh.4 | 8eo8.1 | 8eo8.2 | 8eo8.3 | 8eo8.4 | 8es8.1 | 8es9.1 | 8fja.1 | 8fjb.1 | 8fu4.1 | 8gom.1 | 8gon.1 | 8gvb.1 | 8gvg.1 | 8gvi.1 | 8hn4.1 | 8sbk.1 | 8sbl.1 | 8sbl.2 | 8sbl.3 | 8sbl.4 | 8sgb.1 | 8sgm.1 | 8shi.1 | 8shi.2 | 8sos.1 | 8tbv.1 | 8tbv.2 | 8tbw.1 | 8tbw.2 | 8tuh.1 | 8u9g.1 | 8u9g.2

Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
Medium
High
Extreme

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