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SMTL ID : 6bj2.1

TCR589 in complex with HIV(Pol448-456)/HLA-B35

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.35 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x ILE- PRO- LEU- THR- GLU- GLU- ALA- GLU- LEU: HIV Pol B35 peptide(Non-covalent)

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

34 residues within 4Å:

Chain A: N.96, S.100, N.101, Y.102
Chain B: N.29, Y.49, R.50, R.95
Chain C: Y.7, Y.9, Y.59, R.62, N.63, I.66, F.67, N.70, T.73, E.76, S.77, N.80, L.81, Y.84, R.97, Y.99, T.143, K.146, W.147, V.152, Q.155, L.156, Y.159, L.163, W.167, Y.171

27 PLIP interactions:

20 interactions with chain C, 3 interactions with chain B, 4 interactions with chain A

Hydrophobic interactions: C:Y.59, C:I.66, C:F.67, C:Y.99, C:V.152, C:L.156, C:Y.159, C:L.163, C:W.167, A:Y.102, A:Y.102
Hydrogen bonds: C:Y.7, C:R.62, C:N.70, C:S.77, C:N.80, C:Y.84, C:Y.99, C:K.146, C:Q.155, B:R.95, A:N.96, A:Y.102
Salt bridges: C:R.97, C:K.146, B:R.50, B:R.95

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2:

5 residues within 4Å:

Chain A: D.21, Q.68, T.71, S.73, N.75

1 PLIP interactions:

1 interactions with chain A

Hydrogen bonds: A:T.71

3 x ZN: ZINC ION(Non-covalent)

ZN.3:	2 residues within 4Å: Chain A: D.122 Chain B: H.134 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:D.122, A:D.122, B:H.134
ZN.5:	4 residues within 4Å: Chain B: H.9, H.151, E.153, Y.212 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.9, B:H.151, B:E.153
ZN.6:	1 residues within 4Å: Chain C: E.58 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.58, H₂O.1

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4:

4 residues within 4Å:

Chain B: S.23, F.68, N.70, S.72

3 PLIP interactions:

3 interactions with chain B

Hydrogen bonds: B:N.70, B:S.72, B:S.72

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Sibener, L.V. et al., Isolation of a Structural Mechanism for Uncoupling T Cell Receptor Signaling from Peptide-MHC Binding. Cell (2018)

Release Date

2018-07-25

Peptides

TCR 589 alpha chain: A
TCR 589 beta chain: B
HLA class I histocompatibility antigen, B-35 alpha chain: C
Beta-2-microglobulin: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
A

D
B

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

TCR 589 alpha chain

TCR 589 beta chain

HLA class I histocompatibility antigen, B-35 alpha chain

Beta-2-microglobulin

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1a1m.1 | 1a1n.1 | 1a1o.1 | 1a6z.1 | 1a6z.2 | 1agb.1 | 1agc.1 | 1agd.1 | 1age.1 | 1agf.1 | 1akj.1 | 1c16.1 | 1c16.2 | 1c16.3 | 1c16.4 | 1c16.5 | 1de4.1 | 1de4.2 | 1e27.1 | 1e28.1 | 1exu.1 | 1hsa.1 | 1hsa.2 | 1hsb.1 | 1m05.1 | 1m05.2 | 1m6o.1 | 1mi5.1 | 1n2r.1 | 1onq.1 more...less...

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Background

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