Research workbench

Porcine odorant binding protein complexed with diphenylmethanone

Analyse Porcine odorant binding protein complexed with diphenylmethanone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1DZP
Type: protein
Length: 296 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Odorant-binding protein
UniProt: P81245
Ligands: BZQ
Pockets: 4 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 15% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Odorant-binding protein	protein	149	15% helix, 50% strand	P81245
B	Odorant-binding protein	protein	147	16% helix, 50% strand	P81245

Ligands and binding sites

BZQ · Diphenylmethanone · ligand · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	180	0.85	0.99	22	BZQ
2	171	0.85	0.99	22	BZQ
3	334	0.66	0.81	46	empty
4	116	0.45	0.78	24	empty

Interfaces

1 interface between chains.

A–B · 834 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

1DZP · Porcine Odorant Binding Protein Complexed with diphenylmetha · the same entry in another collection · chain A against A, TM-score 1.00
P81245 · AlphaFold monomer V2.0 prediction for odorant-binding protein (P81245) · a predicted model of the same protein · chain B against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P81245
Elsewhere: RCSB PDB 1DZP · PDBe 1DZP · UniProt P81245

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