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Structure of rhamnosidase from novosphingobium sp. PP1Y

Analyse Structure of rhamnosidase from novosphingobium sp. PP1Y in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Q2F
Type: protein
Length: 1,055 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycoside hydrolase family protein
UniProt: F6IEX3
Ligands: NA
Pockets: 11 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 23% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycoside hydrolase family protein	protein	1055	23% helix, 32% strand	F6IEX3

Ligands and binding sites

NA · Sodium ion · metal · chains A

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

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	465	0.69	0.80	45	empty
2	633	0.68	0.77	59	empty
3	276	0.65	0.82	42	empty
4	470	0.65	0.77	46	empty
5	111	0.52	0.82	23	empty

Modifications

Observed in the structure: 19 modified (engineered).

Compared structures

6Q2F · Structure of Rhamnosidase from Novosphingobium sp. PP1Y · 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 F6IEX3
Elsewhere: RCSB PDB 6Q2F · PDBe 6Q2F · UniProt F6IEX3

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