SMTL ID : 9nph.1

X-ray crystal structure of recombinant Can f 1 in complex with human IgE mAb 1J11 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 2 residues within 4Å: Chain A: N.19 Ligands: SO4.7 No protein-ligand interaction detected (PLIP)

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 4 residues within 4Å: Chain A: D.138, Q.167, S.168 Chain B: H.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.168 EPE.9: 6 residues within 4Å: Chain B: G.26, F.27, T.28, N.74, S.75, D.77 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.26, B:S.75 Salt bridges: B:D.77, B:D.77

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

SO4.3: 3 residues within 4Å: Chain A: Y.48, E.52 Ligands: SO4.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.48, A:Y.48 Water bridges: A:R.53 SO4.4: 2 residues within 4Å: Chain A: K.149, Q.194 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.194 Salt bridges: A:K.149 SO4.5: 3 residues within 4Å: Chain A: V.155, K.156, A.157 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.156, A:A.157 SO4.6: 1 residues within 4Å: Chain A: N.169 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.171, A:K.171 Salt bridges: A:K.171 SO4.7: 1 residues within 4Å: Ligands: NAG.1 No protein-ligand interaction detected (PLIP) SO4.8: 4 residues within 4Å: Chain A: S.66, G.67, N.68, T.69 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.68, A:N.68, A:T.69, A:T.69 SO4.10: 4 residues within 4Å: Chain A: Q.49 Chain B: R.106 Chain C: V.4 Ligands: SO4.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.106 Hydrogen bonds: A:Q.49 SO4.11: 4 residues within 4Å: Chain A: K.163 Chain B: P.41, G.42, R.121 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.42 Salt bridges: B:R.121, A:K.163 SO4.12: 3 residues within 4Å: Chain B: R.30, R.72, N.74 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.72 Salt bridges: B:R.30, B:R.72 SO4.13: 4 residues within 4Å: Chain B: S.31, F.103, V.104, K.105 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.31 SO4.14: 3 residues within 4Å: Chain B: S.174, G.175, V.176 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.174, B:G.175, B:V.176 SO4.15: 2 residues within 4Å: Chain B: M.93, R.121 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.121 SO4.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khatri, K. et al., Human IgE monoclonal antibodies define two unusual epitopes trapping dog allergen Can f 1 in different conformations. Protein Sci. (2025)

Release Date

2025-08-27

Peptides

1J11 Fab light chain: A
1J11 Fab heavy chain: B
Major allergen Can f 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

1J11 Fab light chain

1J11 Fab heavy chain

Major allergen Can f 1

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