SMTL ID : 4u1n.1

HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential HIV-1 escape through identical epitopes

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ARG- PRO- GLN- VAL- PRO- LEU- ARG- PRO- MET: Protein Nef(Non-covalent)

ARG-PRO-GLN-VAL-PRO-LEU-ARG-PRO-MET.1: 32 residues within 4Å: Chain A: M.6, Y.8, Y.60, R.63, N.64, I.67, Y.68, A.70, Q.71, T.74, E.77, S.78, N.81, L.82, Y.85, L.96, Y.100, N.115, Y.117, Y.124, T.144, W.148, A.151, V.153, Q.156, D.157, Y.160, T.164, W.168, Y.172 Ligands: EDO.2, EDO.15 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:I.67, A:I.67, A:A.70, A:E.77, A:Y.100, A:A.151, A:V.153, A:V.153, A:Q.156, A:Y.160, A:Y.160, A:T.164, A:W.168 Hydrogen bonds: A:Y.8, A:N.64, A:S.78, A:N.81, A:Y.100, A:Y.100, A:N.115, A:T.144, A:D.157, A:Y.160, A:Y.172 Water bridges: A:Q.71, A:Y.85, A:W.168 Salt bridges: A:K.147

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 9 residues within 4Å: Chain A: Q.71, T.74, D.75, S.78, L.96, Y.117, W.148 Ligands: ARG-PRO-GLN-VAL-PRO-LEU-ARG-PRO-MET.1, EDO.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.75, A:S.78 Water bridges: A:Y.117 EDO.3: 4 residues within 4Å: Chain A: N.128, E.129, D.130, S.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.129, A:D.130, A:D.130 EDO.4: 7 residues within 4Å: Chain A: H.4, L.180, E.181, R.182, A.183, P.211, E.265 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.181 EDO.5: 7 residues within 4Å: Chain A: D.123, Y.124, I.125, A.126, T.135, A.136, A.137 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.116, A:I.125 EDO.6: 5 residues within 4Å: Chain A: F.37, S.39, P.44, A.72, R.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.73 EDO.7: 7 residues within 4Å: Chain A: P.236, A.237, G.238, D.239, R.240, T.241, F.242 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.237, A:G.238, A:D.239, A:R.240, A:T.241 EDO.8: 3 residues within 4Å: Chain A: E.167, W.168, R.171 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.167, A:R.171 Water bridges: A:R.171 EDO.9: 4 residues within 4Å: Chain A: R.7, M.99, H.114, Q.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.7, A:Q.116 EDO.10: 6 residues within 4Å: Chain A: Y.86, Y.119, K.122, D.123, Y.124, D.138 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.123 Water bridges: A:D.120, A:D.120, A:D.138 EDO.11: 4 residues within 4Å: Chain A: R.36, E.47, P.48, R.49 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.49 EDO.14: 9 residues within 4Å: Chain A: W.205, L.207, R.235, Q.243 Chain B: Y.11, S.12, H.14, P.15, M.100 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.12, B:H.14, A:R.235, A:Q.243 EDO.15: 7 residues within 4Å: Chain A: Y.117, W.148, V.153, D.157 Ligands: ARG-PRO-GLN-VAL-PRO-LEU-ARG-PRO-MET.1, ARG-PRO-GLN-VAL-PRO-LEU-ARG-PRO-MET.1, EDO.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.157 Water bridges: A:N.115

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 6 residues within 4Å: Chain A: S.5, R.7, F.9, Y.28, D.30, D.31 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:Y.28, B:Y.64 GOL.13: 3 residues within 4Å: Chain A: E.181, R.182, A.183 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klverpris, H.N. et al., A molecular switch in immunodominant HIV-1-specific CD8 T-cell epitopes shapes differential HLA-restricted escape. Retrovirology (2015)

Release Date

2015-04-08

Peptides

HLA class I histocompatibility antigen, B-42 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-42 alpha chain

Beta-2-microglobulin

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