SMTL ID : 7nza.1

Structure of OBP1 from Varroa destructor, form P2<1>

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: K.118, H.119, D.120, D.121, N.124 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.120, A:D.121, A:N.124 Salt bridges: A:H.119 SO4.4: 5 residues within 4Å: Chain B: K.118, H.119, D.120, D.121, N.124 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.120, B:D.121, B:N.124 Salt bridges: B:H.119

2 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.2: 13 residues within 4Å: Chain A: P.14, I.16, W.18, P.26, R.31, D.134, I.137, S.138, I.143 Chain B: T.9, P.10, A.11, K.12 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.137, A:I.143, B:T.9 Salt bridges: A:R.31 Hydrogen bonds: B:K.12 Water bridges: B:T.9, B:P.10 NHE.5: 12 residues within 4Å: Chain A: T.9, P.10, A.11, K.12 Chain B: P.14, I.16, W.18, P.26, D.134, I.137, S.138, I.143 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.9, B:I.137, B:I.143 Hydrogen bonds: A:P.10, A:K.12

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

NA.3: 4 residues within 4Å: Chain A: R.88, L.105, H.108, D.109 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.88, A:R.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Amigues, B. et al., A new non-classical fold of varroa odorant-binding proteins reveals a wide open internal cavity. Sci Rep (2021)

Release Date

2021-07-07

Peptides

Odorant Binding Protein from Varroa destructor, form P2<1>: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Odorant Binding Protein from Varroa destructor, form P2<1>

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