SMTL ID : 5nmh.1

HLA A02 presenting SLYNTIATL

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

hetero-1-1-mer

Ligands

1 x SER- LEU- TYR- ASN- THR- ILE- ALA- THR- LEU: Gag protein(Non-covalent)

SER-LEU-TYR-ASN-THR-ILE-ALA-THR-LEU.1: 25 residues within 4Å: Chain A: M.5, Y.7, F.9, M.45, E.63, R.65, K.66, V.67, H.70, T.73, V.76, D.77, L.81, R.97, Y.99, Y.123, T.143, K.146, W.147, V.152, Q.155, L.156, Y.159, W.167, Y.171 36 PLIP interactions: 36 interactions with chain A Hydrophobic interactions: A:Y.7, A:F.9, A:V.67, A:V.76, A:D.77, A:L.81, A:Y.99, A:Y.123, A:T.143, A:W.147, A:V.152, A:L.156, A:Y.159, A:Y.159, A:Y.159 Hydrogen bonds: A:E.63, A:R.65, A:R.65, A:K.66, A:D.77, A:Y.99, A:W.167, A:Y.171, A:Y.171 Water bridges: A:H.70, A:T.73, A:D.77, A:D.77, A:Y.84, A:R.97, A:R.97, A:K.146, A:K.146, A:Q.155, A:L.156 Salt bridges: A:K.146

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

EDO.2: 6 residues within 4Å: Chain A: K.186, L.206, Q.242 Chain B: R.12, P.14 Ligands: GOL.12 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.12, A:Q.242 EDO.3: 3 residues within 4Å: Chain A: Q.262, H.263, E.264 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.262, A:H.263, A:E.264 Water bridges: A:H.263 EDO.4: 4 residues within 4Å: Chain A: R.21, R.35, D.37, A.40 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.35, A:R.35 EDO.5: 6 residues within 4Å: Chain A: S.13, R.14, G.18, E.19, P.20, R.75 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.14 EDO.6: 3 residues within 4Å: Chain A: E.166, W.167, R.170 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.166, A:E.166, A:R.170 Water bridges: A:R.170 EDO.7: 5 residues within 4Å: Chain A: G.1, H.3, Q.180, T.182, E.264 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.1, A:E.264 Water bridges: A:Q.180, A:E.264 EDO.10: 4 residues within 4Å: Chain B: N.83, H.84, V.85, L.87 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.83, B:H.84, B:L.87 Water bridges: B:V.85

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain A: R.6, F.8, Y.27, D.29, D.30 Chain B: Y.63 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.6, A:D.30, A:D.30, B:Y.63, B:Y.63 Water bridges: A:Y.27 GOL.9: 6 residues within 4Å: Chain A: S.42, R.44, M.45, E.46, P.47, W.60 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.46 Water bridges: A:W.60 GOL.11: 5 residues within 4Å: Chain A: R.21, I.23 Chain B: S.33, D.34, L.64 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.33, B:D.34, B:D.34, A:R.14 Water bridges: B:S.33, B:H.51, B:H.51, A:R.21 GOL.12: 12 residues within 4Å: Chain A: W.204, L.206, R.234, Q.242 Chain B: Y.10, S.11, R.12, H.13, P.14, R.97, M.99 Ligands: EDO.2 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.11, B:R.97, B:M.99, A:R.234, A:Q.242 Water bridges: B:S.11 GOL.13: 1 residues within 4Å: Chain B: E.44 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cole, D.K. et al., Dual Molecular Mechanisms Govern Escape at Immunodominant HLA A2-Restricted HIV Epitope. Front Immunol (2017)

Release Date

2017-11-15

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HLA class I histocompatibility antigen, A-2 alpha chain

Beta-2-microglobulin

Related Entries With Identical Sequence