SMTL ID : 3cyz.1

Dimeric crystal structure of a pheromone binding protein from Apis mellifera in complex with 9-keto-2(E)-decenoic acid at pH 7.0

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

3 x 9OD: (2Z)-9-oxodec-2-enoic acid(Non-covalent)

9OD.1: 6 residues within 4Å: Chain A: M.49, M.86, V.108, W.116, F.117, I.119 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.116, A:F.117, A:F.117, A:F.117 Hydrogen bonds: A:F.117 9OD.6: 6 residues within 4Å: Chain B: L.53, L.74, V.85, A.112, F.117 Ligands: 9OD.7 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.53 9OD.7: 13 residues within 4Å: Chain B: K.17, I.31, D.35, Y.48, M.49, L.52, I.101, L.104, A.105, V.108, V.118, I.119 Ligands: 9OD.6 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.52, B:L.104 Hydrogen bonds: B:Y.48, B:Y.48 Water bridges: B:K.17, B:K.17, B:D.35 Salt bridges: B:K.17

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

CL.2: 2 residues within 4Å: Chain A: H.24, C.47 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: D.96 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: A.63, N.64, V.65, P.91, T.92 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: N.64, V.65, P.91, T.92 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain B: E.67, Q.83, M.86, G.87, L.90 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.67, B:Q.83, B:L.90, B:L.90 GOL.10: 2 residues within 4Å: Chain A: E.15 Chain B: L.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pesenti, M.E. et al., Queen bee pheromone binding protein pH-induced domain swapping favors pheromone release. J.Mol.Biol. (2009)

Release Date

2009-04-28

Peptides

Pheromone-binding protein ASP1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pheromone-binding protein ASP1

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