SMTL ID : 8bxv.1

Crystal structure of Odorant Binding Protein 5 from Anopheles gambiae (AgamOBP5) with Thymol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x PGR: R-1,2-PROPANEDIOL(Non-covalent)

PGR.1: 5 residues within 4Å: Chain A: C.18, K.21, C.49, Q.52, M.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.21, A:C.49, A:M.53

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

MPD.2: 6 residues within 4Å: Chain A: M.72, M.80, L.112, V.119, F.120, L.121 No protein-ligand interaction detected (PLIP)

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 7 residues within 4Å: Chain A: S.90, C.91, D.93, V.94, R.97, C.111, Y.115 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.90, A:R.97, A:R.97 Water bridges: A:V.94, A:C.111

1 x IPB: 5-METHYL-2-(1-METHYLETHYL)PHENOL(Non-covalent)

IPB.4: 7 residues within 4Å: Chain A: I.63, T.68, I.88, T.105, S.108, T.109, L.112 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.63, A:I.63, A:T.68, A:I.88 Hydrogen bonds: A:T.109, A:T.109

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

NA.5: 2 residues within 4Å: Chain A: E.86, Y.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.86, A:E.86, A:Y.115 NA.6: 3 residues within 4Å: Chain A: V.65, R.92, Q.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.92, A:Q.95 Water bridges: A:Q.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liggri, P.G.V. et al., The structure of AgamOBP5 in complex with the natural insect repellents Carvacrol and Thymol: Crystallographic, fluorescence and thermodynamic binding studies. Int.J.Biol.Macromol. (2023)

Release Date

2023-03-22

Peptides

Odorant binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Odorant binding protein

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