SMTL ID : 4a87.1

Crystal Structure of Major Birch Pollen Allergen Bet v 1 a in complex with naringenin.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.24 Å

Oligo State

monomer

Ligands

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.1: 6 residues within 4Å: Chain A: F.58, F.64, P.90, A.135, S.136, M.139 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.58, A:F.64, A:P.90, A:M.139 MPD.10: 7 residues within 4Å: Chain A: D.27, F.30, K.54, D.69, Y.81, Y.83 Ligands: NAR.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.30, A:K.54, A:D.69, A:Y.81, A:Y.83 Hydrogen bonds: A:Y.81

1 x NAR: NARINGENIN(Non-covalent)

NAR.2: 16 residues within 4Å: Chain A: T.7, T.9, F.22, I.23, F.30, Y.81, Y.83, I.102, I.116, N.118, S.136, K.137, G.140, E.141 Ligands: NA.3, MPD.10 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.22, A:I.23, A:F.30, A:I.102, A:I.116 Hydrogen bonds: A:N.118, A:E.141 Water bridges: A:N.118, A:S.136

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: N.118, S.136, K.137 Ligands: NAR.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.118, A:S.136 Water bridges: A:K.137

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

SO4.4: 2 residues within 4Å: Chain A: R.70, K.97 3 PLIP interactions: 3 interactions with chain A Water bridges: A:S.84 Salt bridges: A:R.70, A:K.97 SO4.5: 3 residues within 4Å: Chain A: T.9, T.10, R.145 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.9, A:T.10, A:R.145 Water bridges: A:T.10 SO4.6: 3 residues within 4Å: Chain A: E.6, T.7, E.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.7, A:T.7, A:E.8 Salt bridges: A:K.137 SO4.7: 2 residues within 4Å: Chain A: K.20, H.76 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.20, A:H.76 SO4.8: 3 residues within 4Å: Chain A: S.39, P.59, E.60 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.60 Water bridges: A:S.39, A:F.58 SO4.9: 3 residues within 4Å: Chain A: E.131, K.134, E.138 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kofler, S. et al., Crystallographically Mapped Ligand Binding Differs in High and Low Ige Binding Isoforms of Birch Pollen Allergen Bet V 1. J.Mol.Biol. (2012)

Release Date

2012-05-30

Peptides

MAJOR POLLEN ALLERGEN BET V 1-A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

MAJOR POLLEN ALLERGEN BET V 1-A

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