SMTL ID : 7mlh.2 (1 other biounit)

Crystal structure of human IgE (2F10) in complex with Der p 2.0103

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: K.6, D.7, H.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.7, A:D.7 Water bridges: A:D.7 Salt bridges: A:H.11 SO4.2: 4 residues within 4Å: Chain A: R.31 Chain C: N.30, T.31, Y.102 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.30 Salt bridges: A:R.31 SO4.3: 4 residues within 4Å: Chain A: P.26, T.123, H.124, K.126 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.126, A:K.126 Salt bridges: A:H.124, A:K.126 SO4.4: 4 residues within 4Å: Chain B: Y.49, T.53 Chain C: S.103, G.104 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.104, B:Y.49 SO4.5: 2 residues within 4Å: Chain B: P.59, S.60 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.60, B:S.60 Water bridges: B:V.58 SO4.6: 3 residues within 4Å: Chain B: K.156, A.157, G.158 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.158 Water bridges: B:V.159, B:V.159 SO4.9: 4 residues within 4Å: Chain C: R.57, G.58, Y.60, T.69 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.58, C:G.58, C:Y.60 Salt bridges: C:R.57 SO4.10: 2 residues within 4Å: Chain C: S.16, S.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.17 SO4.11: 4 residues within 4Å: Chain C: Y.32, R.98, G.106, Y.108 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.32, C:Y.108, C:Y.108 Water bridges: C:G.106, C:G.106 Salt bridges: C:R.98 SO4.12: 5 residues within 4Å: Chain C: E.10, K.12, S.17, V.18, K.19 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.19 Water bridges: C:K.12 Salt bridges: C:K.12

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

CL.7: 2 residues within 4Å: Chain B: G.107, Y.140 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: T.96, F.97 Chain C: E.46, W.47 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khatri, K. et al., Human IgE monoclonal antibody recognition of mite allergen Der p 2 defines structural basis of an epitope for IgE cross-linking and anaphylaxis in vivo. Pnas Nexus (2022)

Release Date

2022-05-04

Peptides

Der p 2 variant 3: A
IgE Light Chain: B
IgE Heavy chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
E

Der p 2 variant 3

IgE Light Chain

IgE Heavy chain

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