SMTL ID : 8g4p.1

Crystal structure of the peanut allergen Ara h 2 bound by two neutralizing antibodies 13T1 and 13T5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 3 residues within 4Å: Chain A: E.56, S.57, T.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.56, A:T.58 EDO.8: 3 residues within 4Å: Chain C: Q.5, R.117, T.163 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.117, C:R.117 EDO.9: 7 residues within 4Å: Chain C: Q.39, P.40, A.41, T.90, A.91, L.92, L.120 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.40 EDO.13: 8 residues within 4Å: Chain C: Q.39 Chain D: Q.38, K.39, P.40, F.83, A.84, T.85, E.165 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.84, D:T.85 EDO.14: 3 residues within 4Å: Chain D: S.52, S.65, G.66 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.66 EDO.16: 10 residues within 4Å: Chain C: Y.109 Chain D: S.30, R.31, G.50, A.51, S.52, G.66, S.67, G.68, F.71 1 PLIP interactions: 1 interactions with chain D Water bridges: D:S.30

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

CL.2: 3 residues within 4Å: Chain A: F.27, K.28, Y.32 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: P.134 Chain B: S.123, D.124, E.125 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: T.100 Chain B: A.55, A.56 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain C: R.50, W.110 Chain E: N.71 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain C: S.173, G.174 Chain D: K.169 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain C: G.27, S.28 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain D: S.121, D.122, E.123 Ligand excluded by PLIP

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

SO4.3: 7 residues within 4Å: Chain A: S.7, G.9, G.117, T.118, T.119, P.160, K.212 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.117, A:T.119 Water bridges: A:G.8 SO4.6: 2 residues within 4Å: Chain B: K.39, E.81 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.39 SO4.17: 2 residues within 4Å: Chain D: P.59, S.60 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.60, D:S.60 Water bridges: D:R.61 SO4.18: 10 residues within 4Å: Chain B: T.28, V.29, S.30, S.31 Chain C: S.30 Chain E: N.16, R.18, P.19, Q.22, R.65 6 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C, 2 interactions with chain E Hydrogen bonds: B:T.28, B:S.30, B:S.31, C:S.30, E:N.16 Salt bridges: E:R.65

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

NAG.7: 10 residues within 4Å: Chain C: R.38, E.46, W.47, N.60, S.62, L.63 Chain D: D.1, P.95, R.96, T.97 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:R.38, C:E.46, C:W.47, C:N.60 Hydrophobic interactions: D:P.95, D:T.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Min, J. et al., Design of an Ara h 2 hypoallergen from conformational epitopes. Clin Exp Allergy (2024)

Release Date

2023-12-20

Peptides

13t1 Fab heavy chain: A
13T1 Fab light chain: B
13T5 Fab heavy chain: C
13T5 Fab light chain: D
Ara h 2 allergen: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
A

D
B

E
E

13t1 Fab heavy chain

13T1 Fab light chain

13T5 Fab heavy chain

13T5 Fab light chain

Ara h 2 allergen

Related Entries With Identical Sequence