SMTL ID : 3o4l.1

Genetic and structural basis for selection of a ubiquitous T cell receptor deployed in Epstein-Barr virus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.54 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x GLY- LEU- CYS- THR- LEU- VAL- ALA- MET- LEU: BSLF2/BMLF1 protein(Non-covalent)

GLY-LEU-CYS-THR-LEU-VAL-ALA-MET-LEU.1: 35 residues within 4Å: Chain A: M.5, Y.7, F.9, M.45, E.63, K.66, V.67, H.70, T.73, D.77, T.80, L.81, Y.84, Y.99, Y.116, T.143, K.146, W.147, V.152, Q.155, L.156, Y.159, W.167, Y.171 Chain C: Y.26, D.87, N.89, A.90 Chain D: R.97, G.99, T.100, G.101, N.102 Ligands: GOL.12, GOL.14 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:Y.7, A:F.9, A:K.66, A:V.67, A:L.81, A:Y.116, A:W.147, A:Q.155, D:N.102 Hydrogen bonds: A:Y.7, A:E.63, A:D.77, A:Y.99, A:Y.99, A:Y.171, A:Y.171, D:T.100 Water bridges: A:R.97, A:R.97, A:R.97, A:K.146, A:K.146 Salt bridges: A:K.146

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: R.35, A.40 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.35, A:R.35 Water bridges: A:A.41 GOL.3: 3 residues within 4Å: Chain A: K.127, E.128, D.129 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.127, A:E.128, A:D.129 GOL.4: 3 residues within 4Å: Chain A: T.142, H.145, K.146 No protein-ligand interaction detected (PLIP) GOL.8: 3 residues within 4Å: Chain B: Q.3, R.4, T.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.5, B:T.5, B:T.5 GOL.11: 3 residues within 4Å: Chain C: D.118, S.121, S.125 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.118, C:S.125, C:S.125 GOL.12: 8 residues within 4Å: Chain C: D.21, S.23, S.24, T.25, D.87, N.88, N.89 Ligands: GLY-LEU-CYS-THR-LEU-VAL-ALA-MET-LEU.1 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:D.21, C:S.24, C:T.25, C:N.88, C:N.89 Water bridges: C:S.23, C:T.25, C:T.25, C:Y.26 GOL.13: 8 residues within 4Å: Chain D: S.89, S.90, R.111, L.112, T.113, P.153, D.154, Y.189 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.111, D:D.154, D:Y.189, D:Y.189 GOL.14: 11 residues within 4Å: Chain A: Q.155 Chain C: Y.28, D.87, A.90 Chain D: R.97, G.101, N.102, Y.104 Ligands: GLY-LEU-CYS-THR-LEU-VAL-ALA-MET-LEU.1, GLY-LEU-CYS-THR-LEU-VAL-ALA-MET-LEU.1, GLY-LEU-CYS-THR-LEU-VAL-ALA-MET-LEU.1 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Y.28, D:R.97, D:G.101, D:Y.104 GOL.15: 3 residues within 4Å: Chain D: S.219, N.221, D.222 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.219, D:N.221, D:D.222 Water bridges: D:N.221 GOL.16: 3 residues within 4Å: Chain D: F.28, Q.29, G.99 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.29, D:G.99 GOL.17: 6 residues within 4Å: Chain D: W.10, V.11, I.12, H.155, Y.216, G.217 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:I.12, D:H.155, D:G.217 Water bridges: D:I.12, D:S.219, D:T.233

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

SO4.5: 2 residues within 4Å: Chain A: R.219, R.256 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.219, A:R.256 SO4.6: 3 residues within 4Å: Chain A: E.232, T.233, K.243 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.233, A:T.233 Water bridges: A:K.243 Salt bridges: A:K.243 SO4.9: 2 residues within 4Å: Chain A: R.21 Chain B: H.52 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:R.21, B:Y.67 Salt bridges: A:R.21, B:H.52 SO4.10: 3 residues within 4Å: Chain B: N.18, E.75, R.98 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.18, B:N.18 Salt bridges: B:R.98 SO4.18: 4 residues within 4Å: Chain D: E.166, V.167, H.168, S.169 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.168, D:S.169 SO4.19: 5 residues within 4Å: Chain C: K.124 Chain D: T.149, G.150, E.180, R.188 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.180 Salt bridges: D:R.188, C:K.124 SO4.20: 4 residues within 4Å: Chain D: H.7, P.8, S.9, W.10 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.9, D:W.10 Salt bridges: D:H.7

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.7: 3 residues within 4Å: Chain B: S.58, K.59, D.60 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.58, B:K.59, B:D.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miles, J.J. et al., Genetic and structural basis for selection of a ubiquitous T cell receptor deployed in Epstein-Barr virus infection. Plos Pathog. (2010)

Release Date

2011-01-12

Peptides

MHC class I antigen: A
Beta-2-microglobulin: B
T-CELL RECEPTOR, ALPHA CHAIN: C
T-CELL RECEPTOR, BETA CHAIN: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

MHC class I antigen

Beta-2-microglobulin

T-CELL RECEPTOR, ALPHA CHAIN

T-CELL RECEPTOR, BETA CHAIN

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