Research workbench

NAVAB1P detergent (dm)

Analyse NAVAB1P detergent (dm) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7PGG
Type: protein
Length: 294 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ion transport protein
UniProt: Q0VNY2
Ligands: VVA
Pockets: 4 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 85% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Ion transport protein	protein	147	85% helix, 0% strand	Q0VNY2

Ligands and binding sites

VVA · 2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}ethyl heptadecanoate · ligand · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	313	0.65	0.80	27	VVA
2	127	0.42	0.76	20	empty
3	65	0.31	0.75	14	empty
4	85	0.31	0.73	18	empty

Interfaces

1 interface between chains.

A–B · 1774 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 22 modified (engineered).

Compared structures

7PGG · NaVAb1p detergent (DM) · 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
Every structure of UniProt Q0VNY2
Elsewhere: RCSB PDB 7PGG · PDBe 7PGG · UniProt Q0VNY2

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