SMTL ID : 3d18.1

Crystal structure of HLA-B*2709 complexed with a variant of the latent membrane protein 2 peptide (LMP2(L)) of epstein-barr virus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ARG- ARG- ARG- TRP- ARG- ARG- LEU- THR- LEU: Latent membrane protein 2(Non-covalent)

ARG-ARG-ARG-TRP-ARG-ARG-LEU-THR-LEU.1: 30 residues within 4Å: Chain A: Y.7, H.9, T.24, E.45, Y.59, R.62, E.63, Q.65, I.66, C.67, T.73, E.76, D.77, T.80, Y.84, Y.99, H.114, Y.123, T.143, K.146, W.147, V.152, Q.155, L.156, Y.159, E.163, W.167, Y.171 Ligands: GOL.2, GOL.9 42 PLIP interactions: 42 interactions with chain A Hydrophobic interactions: A:Y.7, A:Y.59, A:R.62, A:I.66, A:I.66, A:T.73, A:D.77, A:T.80, A:Y.123, A:T.143, A:W.147, A:V.152, A:Y.159, A:Y.159, A:W.167 Hydrogen bonds: A:Y.7, A:T.24, A:T.24, A:T.24, A:R.62, A:E.63, A:T.73, A:D.77, A:Y.99, A:Y.99, A:T.143, A:Q.155, A:Q.155, A:Y.159, A:Y.171 Water bridges: A:R.62, A:R.62, A:K.70, A:T.73, A:E.76, A:T.80, A:Q.155 Salt bridges: A:E.45, A:E.63, A:E.76, A:K.146, A:E.163

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: K.70, N.97, Y.99, H.114, L.156 Ligands: ARG-ARG-ARG-TRP-ARG-ARG-LEU-THR-LEU.1, ARG-ARG-ARG-TRP-ARG-ARG-LEU-THR-LEU.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.70, A:K.70 Water bridges: A:T.73, A:T.73 GOL.3: 3 residues within 4Å: Chain A: E.166, W.167, R.170 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.166, A:R.170 GOL.5: 9 residues within 4Å: Chain A: L.206, R.234, Q.242 Chain B: Y.11, S.12, H.14, P.15, R.98, M.100 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.12, B:R.98, A:R.234, A:Q.242 GOL.6: 6 residues within 4Å: Chain B: D.35, I.36, E.37, N.84, H.85, V.86 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.36, B:N.84 Water bridges: B:D.35, B:V.86 GOL.8: 4 residues within 4Å: Chain B: N.18, G.19, T.74, E.75 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.75, B:E.75 Water bridges: B:K.76 GOL.9: 4 residues within 4Å: Chain A: A.69 Ligands: ARG-ARG-ARG-TRP-ARG-ARG-LEU-THR-LEU.1, ARG-ARG-ARG-TRP-ARG-ARG-LEU-THR-LEU.1, ARG-ARG-ARG-TRP-ARG-ARG-LEU-THR-LEU.1 No protein-ligand interaction detected (PLIP)

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 8 residues within 4Å: Chain A: R.6, F.8, Y.27, D.29, D.30 Chain B: F.57, Y.64 Ligands: MES.7 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Y.64 Water bridges: A:S.4, A:D.30

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

MES.7: 7 residues within 4Å: Chain A: A.211, F.241 Chain B: Y.27, S.58, K.59, Y.64 Ligands: TRS.4 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.27, B:S.58, B:K.59 Water bridges: B:D.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beltrami, A. et al., Crystal structure of HLA-B*2709 complexed with a variant of the latent membrane protein 2 peptide (LMP2(L)) of epstein-barr virus. To be Published

Release Date

2009-05-05

Peptides

HLA class I histocompatibility antigen, B-27 alpha chain: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HLA class I histocompatibility antigen, B-27 alpha chain

Beta-2-microglobulin

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