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SMTL ID : 5xot.1

Crystal structure of pHLA-B35 in complex with TU55 T cell receptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x ILE- PRO- LEU- THR- GLU- GLU- ALA- GLU- LEU: An HIV reverse transcriptase epitope(Non-covalent)

ILE-PRO-LEU-THR-GLU-GLU-ALA-GLU-LEU.1:

36 residues within 4Å:

Chain A: Y.7, Y.9, Y.59, N.63, I.66, F.67, N.70, T.73, Y.74, E.76, S.77, N.80, L.81, Y.84, I.95, R.97, Y.99, Y.123, T.143, K.146, W.147, V.152, Q.155, L.156, Y.159, W.167, Y.171
Chain C: W.30, S.31, G.96, G.97
Chain D: N.28, R.92, R.94, G.95, I.99

31 PLIP interactions:

4 interactions with chain D, 22 interactions with chain A, 5 interactions with chain C

Hydrophobic interactions: D:R.94, A:Y.7, A:Y.59, A:F.67, A:Y.74, A:L.81, A:I.95, A:Y.123, A:T.143, A:V.152, A:L.156, A:Y.159, A:W.167, C:W.30
Hydrogen bonds: D:G.95, A:N.70, A:Y.74, A:S.77, A:Y.99, A:T.143, A:Q.155, A:Y.171, A:Y.171, C:S.31, C:S.31, C:G.97, C:G.97
Water bridges: D:R.94
Salt bridges: D:R.92, A:R.97, A:K.146

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2:	6 residues within 4Å: Chain A: R.6, F.8, Y.27, D.29, D.30 Chain B: Y.63 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.63, B:Y.63, A:D.29
GOL.3:	5 residues within 4Å: Chain A: M.12 Chain B: S.33, D.34, L.54, L.64 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.33, B:D.34
GOL.4:	8 residues within 4Å: Chain A: W.204, L.206, R.234 Chain B: Y.10, S.11, H.13, P.14, M.99 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.234, B:S.11, B:W.95

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Shi, Y. et al., Conserved V delta 1 Binding Geometry in a Setting of Locus-Disparate pHLA Recognition by delta / alpha beta T Cell Receptors (TCRs): Insight into Recognition of HIV Peptides by TCRs. J. Virol. (2017)

Release Date

2017-06-14

Peptides

HLA class I histocompatibility antigen, B-35 alpha chain: A
Beta-2-microglobulin: B
The Delta chain of TU55 TCR: C
The beta chain of TU55 TCR: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

HLA class I histocompatibility antigen, B-35 alpha chain

Beta-2-microglobulin

The Delta chain of TU55 TCR

The beta chain of TU55 TCR

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