SMTL ID : 8vqf.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.11 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: T.17, N.19 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.17 Hydrogen bonds: A:N.19 NAG.13: 4 residues within 4Å: Chain B: T.56 Chain C: T.53, C.60, N.62 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:T.53, C:N.62, B:D.54, B:T.56

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

SO4.2: 1 residues within 4Å: Chain A: R.53 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.53 SO4.3: 2 residues within 4Å: Chain A: R.53, S.62 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.53 SO4.4: 3 residues within 4Å: Chain A: Q.184, S.187, H.188 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.184 Salt bridges: A:H.188 SO4.5: 2 residues within 4Å: Chain A: P.109, K.110 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.110, A:K.110 SO4.6: 4 residues within 4Å: Chain A: A.157, G.158, E.160 Chain B: S.185 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.158, B:S.185 SO4.7: 2 residues within 4Å: Chain B: R.19, Y.80 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.80 Salt bridges: B:R.19 SO4.8: 4 residues within 4Å: Chain B: K.58, H.59, Y.60, K.65 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.58, B:Y.60 Salt bridges: B:H.59, B:K.65 SO4.9: 2 residues within 4Å: Chain B: S.25, G.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.26 SO4.10: 2 residues within 4Å: Chain B: S.216, N.217 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.217 SO4.11: 3 residues within 4Å: Chain B: T.28, R.30, S.31 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.28 Salt bridges: B:R.30 SO4.12: 3 residues within 4Å: Chain B: Q.3, G.26, R.98 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.3 Salt bridges: B:R.98 SO4.14: 4 residues within 4Å: Chain C: L.6, G.7, K.8, D.9 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.8, C:D.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khatri, K. et al., X-ray crystal structure of natural Can f 1 in complex with human IgE 1J11 Fab. To Be Published

Release Date

2025-01-22

Peptides

IgE 1J11 Light chain: A
IgE 1J11 Heavy chain: B
Major allergen Can f 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

IgE 1J11 Light chain

IgE 1J11 Heavy chain

Major allergen Can f 1