SMTL ID : 7s8a.1

STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH MLL(747-755) PHOSPHOPEPTIDE, CUBIC CRYSTAL FORM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLU- PRO- ARG- SEP- PRO- SER- HIS- SER- MET: MLL cleavage product N320 phosphopeptide(Non-covalent)

GLU-PRO-ARG-SEP-PRO-SER-HIS-SER-MET.1: 29 residues within 4Å: Chain A: Y.7, Y.9, R.62, N.63, I.66, Y.67, A.69, Q.70, T.73, E.76, S.77, N.80, Y.84, L.95, Y.99, D.114, Y.116, Y.123, T.143, K.146, W.147, A.150, E.152, Q.155, R.156, Y.159, E.163, W.167, Y.171 42 PLIP interactions: 42 interactions with chain A Hydrophobic interactions: A:Y.7, A:N.63, A:Y.67, A:A.69, A:Y.99, A:T.143, A:Y.159, A:Y.159, A:W.167 Hydrogen bonds: A:Y.7, A:Y.9, A:R.62, A:R.62, A:Q.70, A:T.73, A:E.76, A:S.77, A:N.80, A:Y.84, A:Y.99, A:Y.99, A:Y.116, A:K.146, A:E.152, A:E.152, A:Q.155, A:Y.171, A:Y.171 Water bridges: A:N.63, A:N.63, A:Q.70, A:Q.70, A:Q.70, A:D.114, A:D.114, A:E.152, A:E.163 Salt bridges: A:R.62, A:R.62, A:D.114, A:K.146 pi-Cation interactions: A:Y.99

1 x 12P: DODECAETHYLENE GLYCOL(Non-covalent)

12P.2: 17 residues within 4Å: Chain A: F.8, Y.27, D.29, D.30, R.48, A.211, T.233, P.235, G.237, R.239, F.241 Chain B: Y.27, S.53, Y.64, L.66, Y.68 Ligands: PEG.6 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.30 Water bridges: A:Y.27, A:A.211, B:Y.27, B:Y.64

1 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)

PE8.3: 10 residues within 4Å: Chain A: R.14, R.17, R.21, D.39 Chain B: S.34, D.35, H.52, L.55, L.65, Y.67 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.14, A:R.17, A:R.21, A:R.21 Water bridges: A:R.14

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 7 residues within 4Å: Chain A: Y.85, Q.87, Y.118, K.121, D.122, D.137 Chain B: M.1 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.85, B:M.1 Water bridges: A:K.121, A:K.121 PGE.5: 7 residues within 4Å: Chain A: Q.115, D.122, Y.123, A.125, T.134, A.135, A.136 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.115 Water bridges: A:Y.123

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 8 residues within 4Å: Chain A: S.2, H.3, D.29, L.179, A.182, P.210, E.264 Ligands: 12P.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.2, A:E.264 Water bridges: A:D.29

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.7: 8 residues within 4Å: Chain A: F.8, M.98, H.113, Q.115 Chain B: F.57, S.58, K.59, W.61 No protein-ligand interaction detected (PLIP)

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 1 residues within 4Å: Chain A: R.75 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.75, A:R.75, A:R.75 Salt bridges: A:R.75

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.9: 9 residues within 4Å: Chain A: R.17, S.92 Chain B: M.1, D.35, I.36, E.37, N.84, H.85, V.86 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.3, B:N.84 Water bridges: B:V.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patskovsky, Y. et al., Molecular mechanism of phosphopeptide neoantigen immunogenicity. Nat Commun (2023)

Release Date

2022-11-02

Peptides

HLA class I histocompatibility antigen, B-7 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-7 alpha chain

Beta-2-microglobulin

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