MolNFT v1 · #135498 · protein

Crystal structure of a methyltransferase involved in the biosynthesis of gentamicin in complex with (1R,2S,3S,4R,6S)-4,6-diamino-3-{[3- deoxy-3-(methylamino)-alpha-D-GLUCOPYRANOSYL]OXY}-2-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside

5U0T · Putative gentamicin methyltransferase: “Crystal structure of a methyltransferase involved in the biosynthesis of gentamicin in complex with…”. X-ray diffraction, 3 ligands (SAH, 7QM, MG), 1 pocket (best druggability 0.70). MolNFT v1…

PDB: 5U0T
Type: protein
Length: 311 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative gentamicin methyltransferase
UniProt: Q2MG72
Ligands: SAH, 7QM, MG
Pockets: 1 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative gentamicin methyltransferase	protein	311	33% helix, 29% strand	Q2MG72

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · chains A
7QM · (1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-3-(methylamino)-alpha-D-glucopyranosyl]oxy}-2-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside · ligand · chains A
MG · Magnesium ion · metal · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	229	0.70	0.86	41	SAH, 7QM

Compared structures

5U0T · Crystal structure of a methyltransferase involved in the biosynthesis of gentamicin in… · 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 Q2MG72
Elsewhere: RCSB PDB 5U0T · PDBe 5U0T · UniProt Q2MG72

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