SMTL ID : 7kgu.1 (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

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

PEG.1: 3 residues within 4Å: Chain A: K.45, Y.55 Ligands: BTB.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.45, A:L.46

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.2: 8 residues within 4Å: Chain A: G.41, K.42, A.43, K.45 Chain B: W.108, G.109, Q.110 Ligands: PEG.1 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.41, A:A.43, A:A.43, B:W.108 Water bridges: B:Q.110

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

SO4.3: 2 residues within 4Å: Chain A: R.108, T.109 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.109, A:T.109 Water bridges: A:R.108 Salt bridges: A:R.108 SO4.4: 3 residues within 4Å: Chain A: K.39, K.42, K.45 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Q.37, A:K.39 Salt bridges: A:K.39, A:K.42, A:K.45 SO4.5: 2 residues within 4Å: Chain A: K.188, H.189 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.188, A:H.189 SO4.6: 2 residues within 4Å: Chain A: P.40, G.41 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.41 Water bridges: B:G.42 SO4.9: 2 residues within 4Å: Chain B: K.30, Y.31 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.31 Salt bridges: B:K.30 SO4.10: 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:D.73, B:D.73, B:T.74, B:S.75 SO4.11: 3 residues within 4Å: Chain B: R.19, K.76, Y.80 6 PLIP interactions: 6 interactions with chain B Water bridges: B:R.19, B:R.19, B:R.19, B:K.76 Salt bridges: B:R.19, B:K.76 SO4.12: 5 residues within 4Å: Chain A: N.137, N.138 Chain B: G.167, H.169, T.188 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.167, A:N.137, A:N.138 Salt bridges: B:H.169 SO4.13: 5 residues within 4Å: Chain A: 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 SO4.14: 2 residues within 4Å: Chain B: S.63, R.87 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.87

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

PG4.7: 6 residues within 4Å: Chain B: S.7, G.8, G.9, G.111, T.112, L.113 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.8, B:G.9, B:T.112, B:L.113 PG4.8: 2 residues within 4Å: Chain B: N.204, K.211 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.204, B:K.211

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
A

B
B

Light Chain, Fab fragment, IGG

Heavy Chain, Fab, IGG, Fab

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