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Macrolide 2'-phosphotransferase type II - complex with GDP and erythromycin

Analyse Macrolide 2'-phosphotransferase type II - complex with GDP and erythromycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5IGY
Type: protein
Length: 295 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Macrolide 2'-phosphotransferase II
UniProt: O32553
Ligands: GDP, ERY, CA
Pockets: 2 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Macrolide 2'-phosphotransferase II	protein	295	48% helix, 18% strand	O32553

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · chains A
ERY · Erythromycin A · ligand · chains A
CA · Calcium ion · metal · chains A

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	1016	0.78	0.80	71	CA, GDP, ERY
2	53	0.31	0.76	14	empty

Compared structures

5IGY · Macrolide 2'-phosphotransferase type II - complex with GDP and erythromycin · 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 O32553
Elsewhere: RCSB PDB 5IGY · PDBe 5IGY · UniProt O32553

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