MolNFT v1 · #78671 · protein

Crystal structure of aminoglycoside-2''-phosphotransferase type iva tobramycin complex

3SG8 · APH(2'')-id: “Crystal structure of aminoglycoside-2''-phosphotransferase type iva tobramycin complex”. X-ray diffraction, 2 ligands (TOY, CL), 9 pockets (best druggability 0.77). MolNFT v1 #78671 on GenesisL1: 3D structure, binding…

PDB: 3SG8
Type: protein
Length: 596 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: APH(2'')-id
UniProt: O68183
Ligands: TOY, CL
Pockets: 9 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	APH(2'')-id	protein	298	48% helix, 14% strand	O68183

Ligands and binding sites

TOY · Tobramycin · ligand · 2 copies · chains A, B
CL · Chloride ion · ion · 2 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	333	0.77	0.87	43	empty
2	235	0.73	0.87	36	empty
3	153	0.66	0.87	28	empty
4	202	0.65	0.84	29	empty
5	73	0.54	0.86	11	empty

Interfaces

1 interface between chains.

A–B · 1157 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

3SG8 · Crystal Structure of Aminoglycoside-2''-Phosphotransferase Type IVa Tobramycin Complex · 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 O68183
Elsewhere: RCSB PDB 3SG8 · PDBe 3SG8 · UniProt O68183

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