MolNFT v1 · #121353 · protein

Crystal structure of an ANTIBIOTIC_NAT family aminoglycoside acetyltransferase HMB0038 from an uncultured soil metagenomic sample in complex with coenzyme a

5HT0 · Aminoglycoside acetyltransferase HMB0005: “Crystal structure of an ANTIBIOTIC_NAT family aminoglycoside acetyltransferase HMB0038 from an uncultured…”. X-ray diffraction, 2 ligands (COA, SO4), 16 pockets (best druggability 0.80).…

PDB: 5HT0
Type: protein
Length: 1,560 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aminoglycoside acetyltransferase HMB0005
UniProt: A0A059X981
Ligands: COA, SO4
Pockets: 16 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 37% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	Aminoglycoside acetyltransferase HMB0005	protein	259	37% helix, 23% strand	A0A059X981
B, D	Aminoglycoside acetyltransferase HMB0005	protein	260	37% helix, 22% strand	A0A059X981
C, E	Aminoglycoside acetyltransferase HMB0005	protein	261	37% helix, 21% strand	A0A059X981

Ligands and binding sites

COA · Coenzyme A · ligand · 6 copies · chains A, B, C, D, E, F
SO4 · Sulfate ion · ion · 21 copies · chains A, F, B, C, D, E

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

Pockets

16 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	865	0.80	0.83	98	SO4
2	980	0.77	0.80	102	SO4
3	867	0.75	0.79	91	empty
4	546	0.75	0.82	47	empty
5	431	0.64	0.78	51	empty

Interfaces

7 interfaces between chains.

C–D · 960 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 935 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 887 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 526 Å² buried · 1 hydrogen bond · protein-protein
B–F · 426 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5HT0 · Crystal structure of an Antibiotic_NAT family aminoglycoside acetyltransferase HMB0038… · 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 A0A059X981
Elsewhere: RCSB PDB 5HT0 · PDBe 5HT0 · UniProt A0A059X981

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