SMTL ID : 2p5w.1

Crystal structures of high affinity human T-cell receptors bound to pMHC reveal native diagonal binding geometry

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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: 39 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.31, R.93, P.94, L.95, L.96, D.97, G.98, T.99, Y.100 Chain D: N.27, E.29, Y.94, L.95, G.96, N.97 31 PLIP interactions: 20 interactions with chain A, 5 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: A:Y.7, A:F.9, A:K.66, A:K.66, A:V.67, A:L.156, A:Y.159, D:L.95, C:Y.31, C:Y.31 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, D:N.27, D:L.95, D:N.97, C:Y.100 Water bridges: A:K.66, A:T.73, A:R.97, A:Q.155, D:E.29 Salt bridges: A:K.146 pi-Stacking: C:Y.31, C:Y.31, C:Y.100

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

SO4.2: 5 residues within 4Å: Chain A: E.198, D.227, V.248, V.249, P.250 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.198, A:E.198, A:D.227, A:D.227 SO4.3: 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:W.167 Water bridges: A:R.170 SO4.4: 3 residues within 4Å: Chain A: W.107, E.173, Q.180 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.173, A:Q.180 SO4.11: 2 residues within 4Å: Chain B: Q.3, T.87 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.3 SO4.14: 6 residues within 4Å: Chain C: P.114, Y.115, I.116, D.143, S.144, Q.145 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.116, C:S.144, C:Q.145 SO4.19: 2 residues within 4Å: Chain D: R.76, L.78 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.78 Salt bridges: D:R.76

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: F.8, Y.27, D.29, D.30 Chain B: Y.64 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.64 Water bridges: B:Y.64 GOL.6: 4 residues within 4Å: Chain A: A.158, Y.159, T.163 Chain C: L.96 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.163 Water bridges: A:T.163 GOL.7: 6 residues within 4Å: Chain A: S.13, L.78, R.82, G.91, H.93, Y.118 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.13, A:S.13, A:R.82, A:H.93, A:Y.118, A:Y.118 GOL.8: 2 residues within 4Å: Chain A: Y.84, T.142 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.84, A:T.142 GOL.12: 7 residues within 4Å: Chain B: T.74, E.75, D.77, E.78, W.96, D.97, R.98 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.74, B:D.77, B:D.97, B:R.98, B:R.98 Water bridges: B:D.77, B:D.77, B:Y.79 GOL.13: 2 residues within 4Å: Chain B: K.7, I.8 No protein-ligand interaction detected (PLIP) GOL.15: 7 residues within 4Å: Chain C: Y.115, I.116, Q.117, N.118, D.170, F.171, K.172 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.115, C:Q.117, C:N.118, C:N.118, C:D.170, C:K.172 Water bridges: C:N.118 GOL.16: 8 residues within 4Å: Chain C: N.18, L.19, V.20, R.61, N.63, Y.76, I.77, A.78 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.19, C:N.63 GOL.17: 2 residues within 4Å: Chain C: D.120 Chain D: H.135 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:D.120 Water bridges: D:H.135 GOL.18: 6 residues within 4Å: Chain C: S.46, L.47, L.48, L.49, Q.57 Chain D: E.100 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.46, C:L.49, C:Q.57 Water bridges: C:L.47, C:L.49, C:S.59 GOL.21: 5 residues within 4Å: Chain D: L.115, E.220, W.221, T.222, Q.223 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.222, D:T.222, D:Q.223 Water bridges: D:D.114, D:L.115

1 x CA: CALCIUM ION(Non-covalent)

CA.9: 3 residues within 4Å: Chain B: N.84, H.85, L.88 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.85, B:L.88, H2O.10

1 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 6 residues within 4Å: Chain B: P.15, A.16, E.17, K.20, N.22, P.73 No protein-ligand interaction detected (PLIP)

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

EPE.20: 4 residues within 4Å: Chain D: K.116, N.117, Q.223, R.225 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.223 Water bridges: D:D.224, D:D.224 Salt bridges: D:R.225

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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