SMTL ID : 2p5e.1

Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC Reveal Native Diagonal Binding Geometry

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x SER- LEU- LEU- MET- TRP- ILE- THR- GLN- CYS: Cancer/testis antigen 1B(Non-covalent)

SER-LEU-LEU-MET-TRP-ILE-THR-GLN-CYS.1: 41 residues within 4Å: Chain A: 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, T.143, K.146, W.147, V.152, L.156, Y.159, W.167, Y.171 Chain C: Y.32, R.94, P.95, L.96, L.97, D.98, G.99, T.100, Y.101 Chain D: N.26, E.28, Y.93, L.94, G.95, N.96 Ligands: GOL.2, IPA.10 36 PLIP interactions: 24 interactions with chain A, 7 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: A:Y.7, A:F.9, A:K.66, A:V.67, A:Y.99, A:Y.99, A:V.152, A:L.156, A:Y.159, A:Y.159, C:Y.32, C:Y.32, C:R.94, D:L.94 Hydrogen bonds: A:E.63, A:K.66, A:D.77, A:Y.99, A:T.143, A:Y.159, A:W.167, A:Y.171, C:Y.101, D:E.28, D:L.94, D:N.96 Water bridges: A:K.66, A:T.73, A:R.97, A:R.97, A:R.97, D:E.28 Salt bridges: A:K.146 pi-Stacking: C:Y.32, C:Y.32, C:Y.101

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: E.58, Y.59, G.62, E.63, K.66, W.167 Chain C: D.98 Ligands: SER-LEU-LEU-MET-TRP-ILE-THR-GLN-CYS.1 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:E.63, A:E.63, C:D.98 Water bridges: A:K.66 GOL.3: 6 residues within 4Å: Chain A: R.6, F.8, Y.27, D.29, D.30 Chain B: Y.64 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.30, B:Y.64, B:Y.64 GOL.4: 8 residues within 4Å: Chain A: S.11, E.19, P.20, F.22, S.38, S.71, Q.72, R.75 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.11, A:S.38, A:Q.72 Water bridges: A:P.20, A:S.38 GOL.5: 3 residues within 4Å: Chain A: W.107, E.173, Q.180 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.180 GOL.6: 3 residues within 4Å: Chain A: E.166, W.167, R.170 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.166, A:R.170, A:R.170 GOL.9: 7 residues within 4Å: Chain B: T.74, E.75, D.77, E.78, W.96, D.97, R.98 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.75, B:D.77, B:D.97, B:R.98, B:R.98 GOL.16: 6 residues within 4Å: Chain D: L.114, K.115, E.219, W.220, T.221, Q.222 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.221, D:Q.222, D:Q.222 Water bridges: D:K.12 GOL.17: 7 residues within 4Å: Chain D: R.34, V.58, N.60, G.61, Y.62, S.82, Q.83 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.34, D:Q.83 Water bridges: D:R.34

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain B: N.84, H.85, L.88 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.85, B:L.88, H2O.10, H2O.13, H2O.14

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

SO4.8: 4 residues within 4Å: Chain A: R.48 Chain B: H.52, S.53, Y.68 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Y.68 Water bridges: B:D.54, A:R.48, A:R.48, A:R.48, A:R.48 Salt bridges: A:R.48 SO4.11: 6 residues within 4Å: Chain C: P.115, Y.116, I.117, D.144, S.145, Q.146 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.117, C:S.145, C:Q.146, C:Q.146 SO4.12: 6 residues within 4Å: Chain C: Y.116, I.117, Q.118, D.171, F.172, K.173 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.118, C:K.173, C:K.173 Water bridges: C:N.119, C:K.173 SO4.13: 3 residues within 4Å: Chain D: S.16, R.75, L.77 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.16 Salt bridges: D:R.75 SO4.14: 4 residues within 4Å: Chain D: A.225, K.226, V.228, Q.230 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.230, D:Q.230

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.10: 5 residues within 4Å: Chain A: Q.155 Chain C: L.96 Ligands: SER-LEU-LEU-MET-TRP-ILE-THR-GLN-CYS.1, SER-LEU-LEU-MET-TRP-ILE-THR-GLN-CYS.1, SER-LEU-LEU-MET-TRP-ILE-THR-GLN-CYS.1 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.155 Hydrogen bonds: A:Q.155

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

EPE.15: 7 residues within 4Å: Chain D: D.113, K.115, N.116, F.118, W.220, Q.222, R.224 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.116, D:Q.222 Water bridges: D:D.223 Salt bridges: D:R.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sami, M. et al., Crystal structures of high affinity human T-cell receptors bound to peptide major histocompatibility complex reveal native diagonal binding geometry. Protein Eng.Des.Sel. (2007)

Release Date

2007-09-25

Peptides

HLA class I histocompatibility antigen, A-2 alpha chain: A
Beta-2-microglobulin: B
T-Cell Receptor, Alpha Chain: C
Hypothetical protein: 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

T-Cell Receptor, Alpha Chain

Hypothetical protein

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