SMTL ID : 6bj8.1

TCR55 in complex with Pep20/HLA-B35

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x VAL- PRO- LEU- THR- GLU- ASP- ALA- GLU- LEU: VAL-PRO-LEU-THR-GLU-ASP-ALA-GLU-LEU(Non-covalent)

VAL-PRO-LEU-THR-GLU-ASP-ALA-GLU-LEU.1: 39 residues within 4Å: Chain A: M.5, 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, R.97, Y.99, Y.123, T.143, K.146, W.147, V.152, Q.155, L.156, Y.159, L.163, 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 Ligands: GOL.10, GOL.16 44 PLIP interactions: 30 interactions with chain A, 9 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: A:Y.59, A:F.67, A:F.67, A:T.73, A:E.76, A:L.81, A:Y.123, A:W.147, A:V.152, A:L.156, A:Y.159, A:L.163, A:W.167, A:W.167, D:R.94, C:W.30 Hydrogen bonds: A:N.70, A:S.77, A:N.80, A:Y.99, A:T.143, A:Q.155, A:Y.159, A:Y.171, A:Y.171, D:N.28, D:G.95, C:S.31, C:S.31, C:G.97 Water bridges: A:N.70, A:S.77, A:S.77, A:Y.99, A:W.147, D:N.26, D:N.26, D:G.96, D:G.96, C:S.31 Salt bridges: A:R.97, A:K.146, D:K.69, D:R.92

27 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: Q.54, G.56, P.57 Ligand excluded by PLIP GOL.3: 8 residues within 4Å: Chain A: T.31, T.178, L.179, R.181, Y.209, D.238, R.239, T.240 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: R.6, F.8, Y.27, D.29, D.30 Ligand excluded by PLIP GOL.5: 3 residues within 4Å: Chain A: R.219, D.220, E.222 Ligand excluded by PLIP GOL.6: 3 residues within 4Å: Chain A: E.166, W.167, R.170 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: H.191, P.193, A.199, S.251, G.252, E.254 Ligand excluded by PLIP GOL.8: 5 residues within 4Å: Chain A: R.44, T.45, E.46, P.47, W.60 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: R.6, F.8, M.98, H.113, Q.115 Ligand excluded by PLIP GOL.10: 10 residues within 4Å: Chain A: Y.74, R.97, D.114, W.133, W.147, V.152, L.156 Ligands: VAL-PRO-LEU-THR-GLU-ASP-ALA-GLU-LEU.1, VAL-PRO-LEU-THR-GLU-ASP-ALA-GLU-LEU.1, VAL-PRO-LEU-THR-GLU-ASP-ALA-GLU-LEU.1 Ligand excluded by PLIP GOL.11: 7 residues within 4Å: Chain A: R.111, G.112, H.113, D.114, Q.115, L.126, E.128 Ligand excluded by PLIP GOL.13: 9 residues within 4Å: Chain A: W.204, L.206, R.234, Q.242 Chain B: Y.10, S.11, H.13, P.14 Ligands: PO4.12 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain A: I.23, R.35, D.37 Chain B: H.51, D.53, L.54 Ligand excluded by PLIP GOL.15: 8 residues within 4Å: Chain B: I.7, Q.8, V.9, V.93, K.94, W.95, D.96 Ligands: PO4.12 Ligand excluded by PLIP GOL.16: 10 residues within 4Å: Chain A: Q.155 Chain C: S.31, Y.32, Y.33, G.96, Q.99 Chain D: G.96, I.99 Ligands: VAL-PRO-LEU-THR-GLU-ASP-ALA-GLU-LEU.1, VAL-PRO-LEU-THR-GLU-ASP-ALA-GLU-LEU.1 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain C: N.114, I.115, Q.116, N.117, D.169, F.170, K.171 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain A: E.154, R.157, A.158 Chain C: D.54, E.55, Q.56 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain C: L.101, V.102, F.103 Chain D: G.40, L.41, R.42 Ligand excluded by PLIP GOL.22: 4 residues within 4Å: Chain C: K.100 Chain D: Y.45, Y.46, E.57 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain D: Y.45, Y.46, S.47, S.49, G.51, T.52, R.66 Ligand excluded by PLIP GOL.24: 9 residues within 4Å: Chain D: P.37, T.84, S.85, V.86, R.108, L.109, T.110, D.151, H.152 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain D: D.114, K.116, E.220, W.221, T.222, Q.223 Ligand excluded by PLIP GOL.26: 9 residues within 4Å: Chain D: Q.9, V.10, K.12, Q.15, L.115, G.214, L.215, S.216, D.219 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain C: R.126, D.127, S.128, K.129 Chain D: V.125, E.127, E.236 Ligand excluded by PLIP GOL.28: 4 residues within 4Å: Chain D: P.6, K.7, F.8, Y.213 Ligand excluded by PLIP GOL.29: 3 residues within 4Å: Chain D: I.232, V.233, S.234 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain D: S.16, M.17, T.18, R.75 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain D: W.158, V.159, N.160, G.161, H.205, R.207 Ligand excluded by PLIP

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.12: 8 residues within 4Å: Chain A: W.204, R.234, W.244 Chain B: V.9, Y.10, D.96 Ligands: GOL.13, GOL.15 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:R.234, B:S.11 Salt bridges: A:R.234 PO4.20: 6 residues within 4Å: Chain C: M.165, R.166, S.167 Chain D: S.166, G.167, R.193 8 PLIP interactions: 3 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:S.166, D:R.193, C:R.166, C:S.167, C:S.167, C:S.167, C:S.167 Water bridges: D:S.195 PO4.21: 1 residues within 4Å: Chain C: Q.2 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.2, C:Q.2 PO4.32: 5 residues within 4Å: Chain D: K.162, E.163, V.164, H.165, S.166 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.163, D:H.165, D:S.166 Water bridges: D:S.166 Salt bridges: D:K.162

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

HLA class I histocompatibility antigen, B-35 alpha chain: A
Beta-2-microglobulin: B
TCR 55 alpha chain: C
TCR 55 beta chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
H

HLA class I histocompatibility antigen, B-35 alpha chain

Beta-2-microglobulin

TCR 55 alpha chain

TCR 55 beta chain

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