SMTL ID : 7nmg.1

Human MHC Class I, A24 Allele presenting LWM, Complex with 4C6 TCR

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x LEU- TRP- MET- ARG- LEU- LEU- PRO- LEU- LEU: Diabetes epitope LWMRLLPLL(Non-covalent)

LEU-TRP-MET-ARG-LEU-LEU-PRO-LEU-LEU.1: 47 residues within 4Å: Chain A: M.5, Y.7, A.24, M.45, Y.59, E.63, K.66, V.67, H.70, T.73, E.76, N.77, I.80, Y.84, L.95, M.97, F.99, H.114, Y.116, Y.123, T.143, K.146, W.147, V.152, Q.156, Y.159, T.163, G.167, R.170, Y.171 Chain C: D.26, S.28, S.29, Y.31, P.92, S.93, G.94, N.95, T.96, G.97 Chain D: N.29, R.30, Q.49, H.96, H.97 Ligands: EDO.6, SO4.7 34 PLIP interactions: 5 interactions with chain C, 24 interactions with chain A, 5 interactions with chain D Hydrogen bonds: C:S.29, C:P.92, A:Y.7, A:E.63, A:H.70, A:N.77, A:N.77, A:Y.84, A:Q.156, A:Y.171, D:R.30, D:R.30 Water bridges: C:G.94, C:G.94 Salt bridges: C:D.26, A:K.146 Hydrophobic interactions: A:Y.7, A:A.24, A:Y.59, A:K.66, A:K.66, A:V.67, A:H.70, A:T.73, A:E.76, A:I.80, A:I.80, A:L.95, A:W.147, A:V.152, D:N.29, D:Q.49, D:H.97 pi-Stacking: A:F.99

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

SO4.2: 4 residues within 4Å: Chain A: S.2, H.3, S.4, D.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.29 SO4.7: 7 residues within 4Å: Chain A: Q.155, Q.156, Y.159 Chain C: T.30 Ligands: LEU-TRP-MET-ARG-LEU-LEU-PRO-LEU-LEU.1, LEU-TRP-MET-ARG-LEU-LEU-PRO-LEU-LEU.1, LEU-TRP-MET-ARG-LEU-LEU-PRO-LEU-LEU.1 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.155, A:Q.156, C:T.30 Water bridges: A:T.163 SO4.8: 6 residues within 4Å: Chain C: E.5, Q.6, N.21, C.22, T.23, H.71 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.5, C:T.23

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

EPE.3: 6 residues within 4Å: Chain A: P.47, R.48, A.49, P.50, E.53 Chain B: E.51 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.49, A:E.53 Water bridges: A:R.48, A:R.48, B:Y.68

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain B: Q.9, V.10, K.95, D.97, M.100 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.10, B:D.97, B:D.97 EDO.5: 7 residues within 4Å: Chain A: L.206, R.234, Q.242 Chain B: Y.11, S.12, H.14, P.15 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.234, B:S.12 EDO.6: 9 residues within 4Å: Chain A: A.69, T.73 Chain C: N.95 Chain D: R.30, Y.47, Q.49 Ligands: LEU-TRP-MET-ARG-LEU-LEU-PRO-LEU-LEU.1, LEU-TRP-MET-ARG-LEU-LEU-PRO-LEU-LEU.1, LEU-TRP-MET-ARG-LEU-LEU-PRO-LEU-LEU.1 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.30, D:Y.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rizkallahp, P.J. et al., Human MHC Class I, A24 Allele presenting LWM, Complex with 4C6 TCR. To Be Published

Release Date

2022-09-07

Peptides

MHC class I antigen: A
Human MHC Class I, beta 2 microglobulin: B
Human 4C6 T-cell Receptor, alpha Chain: C
Human 4C6 T-cell Receptor, beta Chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

MHC class I antigen

Human MHC Class I, beta 2 microglobulin

Human 4C6 T-cell Receptor, alpha Chain

Human 4C6 T-cell Receptor, beta Chain

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