SMTL ID : 7kgu.4 (3 other biounits)

Structure of 2Q1-Fab, an antibody selective for IDH2R140Q-HLA-B*07:02

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-mer

Ligands

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

PEG.1: 3 residues within 4Å: Chain A: P.14, R.87, A.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.88 Water bridges: A:E.89 PEG.9: 4 residues within 4Å: Chain A: Q.110 Chain B: K.42, A.43, K.45 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.43, B:K.45, B:K.45, A:Q.110, A:Q.110

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

SO4.2: 3 residues within 4Å: Chain A: R.19, K.76, Y.80 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.19, A:R.19, A:R.19, A:K.76 Salt bridges: A:R.19, A:K.76 SO4.3: 4 residues within 4Å: Chain A: A.72, D.73, T.74, S.75 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.73, A:T.74, A:S.75 SO4.4: 4 residues within 4Å: Chain A: S.7, G.8, G.9, T.112 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.8, A:G.9, A:G.9, A:T.112 SO4.5: 2 residues within 4Å: Chain A: K.30, Y.31 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.31, A:Y.31 Salt bridges: A:K.30 SO4.6: 3 residues within 4Å: Chain A: N.204, K.206, K.211 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.204 Salt bridges: A:K.206, A:K.211 SO4.10: 5 residues within 4Å: Chain B: R.24, S.67, G.68, T.69, D.70 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.69, B:D.70 Salt bridges: B:R.24

1 x K: POTASSIUM ION(Non-covalent)

K.7: 4 residues within 4Å: Chain A: V.5, S.7, S.21, A.23 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:V.5, H2O.4

1 x GLY: GLYCINE(Covalent)

GLY.8: 2 residues within 4Å: Chain B: N.210, R.211 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 6 residues within 4Å: Chain B: W.35, A.51, G.64, S.65, F.71, T.72 Ligand excluded by 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

2021-06-23

Peptides

Heavy Chain, Fab, IGG, Fab: A
Light Chain, Fab fragment, IGG: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

Heavy Chain, Fab, IGG, Fab

Light Chain, Fab fragment, IGG

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