SMTL ID : 6uj9.1

Crystal structure of HLA-B*07:02 with R140Q mutant IDH2 peptide in complex with Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

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

PEG.1: 5 residues within 4Å: Chain A: T.135, A.136, A.137, Q.142, Q.145 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.136, A:Q.145 PEG.2: 4 residues within 4Å: Chain A: E.164, E.167, W.168, R.171 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.171 PEG.3: 2 residues within 4Å: Chain A: Q.142, R.146 No protein-ligand interaction detected (PLIP) PEG.10: 5 residues within 4Å: Chain A: R.7, F.9, Y.28, D.30 Chain B: Y.83 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.83 PEG.12: 3 residues within 4Å: Chain A: R.152 Chain D: S.52, L.54 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:R.152, D:L.54 PEG.13: 2 residues within 4Å: Chain D: S.127, G.128 No protein-ligand interaction detected (PLIP)

1 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.4: 7 residues within 4Å: Chain A: D.31, T.32, Q.33, R.49, G.238, R.240, F.242 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.49, A:R.240

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

SO4.5: 6 residues within 4Å: Chain A: E.20, Q.73, R.76, E.77, R.80 Chain E: Y.59 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.20, A:Q.73, A:E.77 Salt bridges: A:R.80 SO4.6: 3 residues within 4Å: Chain A: L.110, E.129, E.162 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.162 SO4.7: 4 residues within 4Å: Chain A: G.84, N.87, Q.88 Chain E: G.54 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.56, E:D.56 SO4.8: 4 residues within 4Å: Chain A: R.80 Chain E: Y.57, T.58, Y.59 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain E Salt bridges: A:R.80 Hydrogen bonds: E:T.58 SO4.9: 1 residues within 4Å: Chain A: E.265 No protein-ligand interaction detected (PLIP) SO4.11: 4 residues within 4Å: Chain B: I.55, E.56, V.57, Y.86 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.57, B:Y.86, B:Y.86 SO4.14: 3 residues within 4Å: Chain E: K.30, Y.55, T.74 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.74 Water bridges: E:T.74 Salt bridges: E:K.30 SO4.15: 2 residues within 4Å: Chain E: Y.55, D.56 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.56

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
Fab light chain: D
Fab heavy chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
L

E
H

HLA class I histocompatibility antigen, B-7 alpha chain

Beta-2-microglobulin

Isocitrate dehydrogenase [NADP], mitochondrial

Fab light chain

Fab heavy chain

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