SMTL ID : 3qfj.1

The complex between TCR A6 and human Class I MHC HLA-A2 with the modified TAX (Y5F) peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x LEU- LEU- PHE- GLY- PHE- PRO- VAL- TYR- VAL: TAX(Y5F) peptide(Non-covalent)

LEU-LEU-PHE-GLY-PHE-PRO-VAL-TYR-VAL.1: 39 residues within 4Å: Chain A: M.5, Y.7, F.9, M.45, Y.59, E.63, K.66, V.67, H.70, Q.72, T.73, V.76, D.77, T.80, Y.84, Y.99, Y.116, T.143, K.146, W.147, V.152, Q.155, L.156, Y.159, T.163, W.167, Y.171 Chain C: G.28, Q.30, S.31, T.92, D.93, S.94 Chain D: E.30, L.97, A.98, G.99, P.102 Ligands: GOL.7 43 PLIP interactions: 35 interactions with chain A, 6 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: A:Y.7, A:Y.7, A:F.9, A:Y.59, A:K.66, A:V.67, A:T.73, A:V.76, A:V.76, A:D.77, A:Y.99, A:Y.116, A:T.143, A:W.147, A:V.152, A:L.156, A:Y.159, A:Y.159, A:T.163, A:W.167, A:W.167, C:Q.30, D:P.102 Hydrogen bonds: A:Y.7, A:E.63, A:Q.72, A:D.77, A:Y.84, A:Y.99, A:Y.99, A:Y.159, A:Y.171, C:Q.30, C:Q.30, C:S.94, D:L.97 Water bridges: A:T.73, A:R.97, A:R.97, A:Y.116, C:D.93, C:S.94 Salt bridges: A:K.146

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: S.105, W.107, Q.180 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.105, A:Q.180 GOL.3: 4 residues within 4Å: Chain A: R.14, P.15, R.17 Chain B: D.35 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:P.15, A:R.17, B:D.35, B:D.35 GOL.4: 4 residues within 4Å: Chain B: P.6, K.7, I.8, K.92 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.6, B:I.8, B:K.92 GOL.5: 5 residues within 4Å: Chain B: E.37, V.38, D.39, R.46, Y.67 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.37, B:V.38, B:Y.67, B:Y.67 GOL.6: 1 residues within 4Å: Chain B: S.89 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.89 GOL.7: 6 residues within 4Å: Chain A: V.76, T.80, Y.84, K.146 Ligands: LEU-LEU-PHE-GLY-PHE-PRO-VAL-TYR-VAL.1, LEU-LEU-PHE-GLY-PHE-PRO-VAL-TYR-VAL.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.80 GOL.8: 3 residues within 4Å: Chain C: D.57, R.59, F.60 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.57, C:R.59, C:R.59 GOL.9: 3 residues within 4Å: Chain D: R.210, S.237, E.239 1 PLIP interactions: 1 interactions with chain D Water bridges: D:S.237 GOL.10: 7 residues within 4Å: Chain D: V.156, L.158, T.173, D.174, P.175, P.177, L.191 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.158, D:L.158 GOL.11: 4 residues within 4Å: Chain D: P.8, K.9, F.10, Y.216 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.9, D:F.10 Water bridges: D:F.10, D:G.217 GOL.12: 3 residues within 4Å: Chain D: M.27, N.28, A.98 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.28 Water bridges: D:N.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scott, D.R. et al., Disparate degrees of hypervariable loop flexibility control T-cell receptor cross-reactivity, specificity, and binding mechanism. J.Mol.Biol. (2011)

Release Date

2012-01-11

Peptides

HLA class I histocompatibility antigen, A-2 alpha chain: A
Beta-2-microglobulin: B
A6 alpha chain: C
A6 beta chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

HLA class I histocompatibility antigen, A-2 alpha chain

Beta-2-microglobulin

A6 alpha chain

A6 beta chain

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