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

Analyse Structure of OBP1 from varroa destructor, form P2<1> in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7NZA
Type: protein
Length: 282 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Odorant binding protein from varroa destructor, form P2<1>
Ligands: NA, SO4
Pockets: 2 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 63% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Odorant binding protein from varroa destructor, form P2<1>	protein	141	63% helix, 4% strand	—

Ligands and binding sites

NA · Sodium ion · metal · chains A
SO4 · Sulfate ion · ion · 2 copies · chains A, B
NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1199	0.80	0.81	102	NHE
2	61	0.34	0.77	14	empty

Interfaces

1 interface between chains.

A–B · 1952 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

7NZA · Structure of OBP1 from Varroa destructor, form P2<1> · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 7NZA · PDBe 7NZA

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