SMTL ID : 6uj8.1 (1 other biounit)

Crystal structure of HLA-B*07:02 with wild-type IDH2 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

PEG.1: 7 residues within 4Å: Chain A: F.9, Y.28, D.30, D.31 Chain B: Y.83 Ligands: 1PE.2, PEG.6 No protein-ligand interaction detected (PLIP) PEG.3: 4 residues within 4Å: Chain A: E.164, E.167, W.168, R.171 No protein-ligand interaction detected (PLIP) PEG.6: 4 residues within 4Å: Chain B: S.77, K.78 Ligands: PEG.1, PGE.7 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.77, B:K.78 Water bridges: A:E.233 PEG.8: 4 residues within 4Å: Chain B: P.25, I.27, L.107, K.111 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.111

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

1PE.2: 9 residues within 4Å: Chain A: Y.28, R.49, T.234, P.236, F.242 Chain B: Y.46, S.72, Y.83 Ligands: PEG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.49 Water bridges: A:G.238

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

SO4.4: 3 residues within 4Å: Chain A: E.233, T.234, K.244 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.234, A:T.234, A:T.234 Water bridges: A:K.244, A:K.244 Salt bridges: A:K.244 SO4.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

PGE.7: 8 residues within 4Å: Chain A: F.9, M.99, Q.116 Chain B: F.76, S.77, K.78, W.80 Ligands: PEG.6 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hwang, M.S. et al., Structural engineering of chimeric antigen receptors targeting HLA-restricted neoantigens. Nat Commun (2021)

Release Date

2021-05-05

Peptides

HLA class I histocompatibility antigen, B-7 alpha chain: A
Beta-2-microglobulin: B
Isocitrate dehydrogenase [NADP], mitochondrial: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

HLA class I histocompatibility antigen, B-7 alpha chain

Beta-2-microglobulin

Isocitrate dehydrogenase [NADP], mitochondrial

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