SMTL ID : 5meo.1

Human Leukocyte Antigen presenting ILGKFLHRL

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ILE- LEU- GLY- LYS- PHE- LEU- HIS- ARG- LEU: ILE-LEU-GLY-LYS-PHE-LEU-HIS-ARG-LEU(Non-covalent)

ILE-LEU-GLY-LYS-PHE-LEU-HIS-ARG-LEU.1: 28 residues within 4Å: Chain A: M.5, Y.7, F.9, M.45, Y.59, E.63, K.66, V.67, H.70, T.73, D.77, T.80, L.81, Y.84, R.97, Y.99, H.114, Y.116, T.143, K.146, W.147, V.152, Q.155, L.156, Y.159, T.163, W.167, Y.171 39 PLIP interactions: 39 interactions with chain A Hydrophobic interactions: A:Y.7, A:F.9, A:Y.59, A:K.66, A:V.67, A:D.77, A:L.81, A:Y.116, A:T.143, A:W.147, A:V.152, A:L.156, A:Y.159, A:T.163, A:W.167, A:W.167 Hydrogen bonds: A:E.63, A:D.77, A:Y.84, A:R.97, A:Y.99, A:Y.99, A:K.146, A:Q.155, A:Y.171 Water bridges: A:K.66, A:K.66, A:H.70, A:H.70, A:D.77, A:D.77, A:T.80, A:R.97, A:K.146, A:Q.155 Salt bridges: A:K.146 pi-Stacking: A:Y.99, A:W.147, A:Y.159

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

EDO.2: 6 residues within 4Å: Chain A: R.6, F.8, Y.27, D.29, D.30 Chain B: Y.64 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.30, B:Y.64 Water bridges: A:S.4, A:Y.27, A:D.29 EDO.3: 7 residues within 4Å: Chain A: H.188, T.190, W.204 Chain B: P.15, R.98, D.99 Ligands: EDO.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.99 EDO.4: 3 residues within 4Å: Chain A: R.14, R.17 Ligands: EDO.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.17, A:R.17 Water bridges: A:R.14, A:R.14 EDO.5: 6 residues within 4Å: Chain A: R.14, E.19, P.20, R.21, S.38, D.39 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.14, A:R.14, A:E.19, A:S.38, A:D.39, A:D.39 EDO.6: 7 residues within 4Å: Chain A: Y.85, Y.118, K.121, D.122, Y.123, A.136, D.137 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.121, A:K.121 EDO.7: 3 residues within 4Å: Chain A: V.76, G.79, T.80 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.75, A:G.79 EDO.8: 4 residues within 4Å: Chain A: E.55, G.56, P.57, W.60 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.55 EDO.9: 4 residues within 4Å: Chain A: W.107, E.173, K.176, Q.180 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.180, A:Q.180 EDO.10: 2 residues within 4Å: Chain A: D.122, A.125 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:D.122, B:W.61 EDO.11: 8 residues within 4Å: Chain A: V.12, S.13, R.14, R.17, R.21, S.92 Chain B: D.35 Ligands: EDO.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.14, A:R.14, A:R.17, A:S.92 Water bridges: A:S.92 EDO.17: 7 residues within 4Å: Chain A: F.8, M.98, Q.115 Chain B: F.57, S.58, K.59, W.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.115 EDO.18: 8 residues within 4Å: Chain A: L.206, R.234, Q.242 Chain B: Y.11, S.12, H.14, P.15 Ligands: EDO.3 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.12, B:H.14, B:M.100, A:R.234 EDO.19: 6 residues within 4Å: Chain A: V.231, R.234, W.244 Chain B: Q.9, V.10, M.100 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.234, B:V.10, B:V.10, B:M.100 EDO.20: 3 residues within 4Å: Chain B: K.95, W.96, D.97 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.96 EDO.21: 3 residues within 4Å: Chain B: P.6, K.7, I.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.8

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 3 residues within 4Å: Chain A: R.35, A.40, A.41 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.35, A:R.35, A:A.41 Water bridges: A:S.42 GOL.13: 3 residues within 4Å: Chain A: Q.87, S.88, H.93 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.87, A:S.88 Water bridges: A:S.88, A:H.93 GOL.14: 3 residues within 4Å: Chain A: G.16, R.17, G.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.16, A:R.17, A:G.18 GOL.22: 7 residues within 4Å: Chain B: E.37, V.38, D.39, R.82, V.83, N.84, P.91 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.37, B:D.39, B:D.39 Water bridges: B:R.46

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

SO4.15: 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 SO4.16: 3 residues within 4Å: Chain A: R.21, D.39 Chain B: H.52 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:H.52, A:R.21 Water bridges: A:R.21, A:D.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cole, D.K. et al., Structural Mechanism Underpinning Cross-reactivity of a CD8+ T-cell Clone That Recognizes a Peptide Derived from Human Telomerase Reverse Transcriptase. J. Biol. Chem. (2017)

Release Date

2016-12-07

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

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