SMTL ID : 7kgu.2 (3 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-mer

Ligands

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

PEG.1: 4 residues within 4Å: Chain A: S.7, P.8, S.9, S.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.7, A:S.9, A:S.10 PEG.5: 3 residues within 4Å: Chain B: S.17, L.18, R.19 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.17, B:R.19, B:R.19 Water bridges: B:R.19, B:S.21 PEG.6: 6 residues within 4Å: Chain B: S.7, G.8, G.9, G.111, T.112, L.113 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.8, B:L.113

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

SO4.2: 4 residues within 4Å: Chain A: Q.37, K.39, K.42, K.45 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.39, A:K.42, A:K.45 SO4.3: 6 residues within 4Å: Chain A: F.96, T.97, F.98 Chain B: L.45, E.46, W.47 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.45, B:W.47, A:F.98 SO4.4: 3 residues within 4Å: Chain A: T.5, R.24, S.26 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.5 Salt bridges: A:R.24 SO4.7: 2 residues within 4Å: Chain B: K.30, Y.31 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.30 SO4.8: 4 residues within 4Å: Chain B: F.27, N.28, Y.31, Y.32 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.28, B:Y.32 Water bridges: B:G.26 SO4.9: 3 residues within 4Å: Chain B: N.204, K.206, K.211 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.204 Water bridges: B:K.211, B:K.211 Salt bridges: B:K.206, B:K.211 SO4.10: 3 residues within 4Å: Chain B: R.19, K.76, Y.80 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Y.80 Salt bridges: B:R.19, B:K.76 SO4.11: 4 residues within 4Å: Chain A: N.137, N.138 Chain B: G.167, H.169 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.137, A:N.138, B:G.167 Salt bridges: B:H.169 SO4.12: 4 residues within 4Å: Chain B: A.72, D.73, T.74, S.75 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.72, B:D.73, B:T.74, B:S.75 SO4.13: 3 residues within 4Å: Chain B: R.87, A.88, E.89 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.88 SO4.14: 1 residues within 4Å: Chain B: K.122 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.121

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Light Chain, Fab fragment, IGG

Heavy Chain, Fab, IGG, Fab

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