SMTL ID : 6vr2.1

Aminoglycoside N-2'-Acetyltransferase-Ia [AAC(2')-Ia] in complex with acetylated-tobramycin and CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

2 x R7Y: (1S,2S,3R,4S,6R)-3-{[2-(acetylamino)-6-amino-2,3,6-trideoxy-alpha-D-ribo-hexopyranosyl]oxy}-4,6-diamino-2-hydroxycycloh exyl 3-amino-3-deoxy-alpha-D-glucopyranoside(Non-covalent)

R7Y.1: 16 residues within 4Å: Chain A: F.29, D.32, F.33, D.37, V.78, E.79, A.80, M.81, S.114, S.116, D.117, Y.123, E.149, D.176, W.178 Ligands: COA.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:D.32, A:E.79, A:A.80, A:M.81, A:S.114, A:D.117, A:D.117, A:E.149, A:W.178 Water bridges: A:E.79, A:S.114, A:R.173, A:D.176 R7Y.5: 16 residues within 4Å: Chain B: F.29, D.32, F.33, D.37, E.79, A.80, M.81, S.114, S.116, D.117, Y.123, E.148, E.149, D.176, W.178 Ligands: COA.6 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:D.32, B:E.79, B:A.80, B:M.81, B:S.114, B:D.117, B:D.117, B:E.148, B:E.149, B:W.178 Water bridges: B:S.34, B:E.79, B:S.114, B:R.173, B:D.176

2 x COA: COENZYME A(Non-covalent)

COA.2: 18 residues within 4Å: Chain A: G.28, F.29, M.81, V.82, V.83, R.88, R.89, Q.90, G.91, I.92, G.93, R.94, A.115, S.116, K.121, L.122, Y.123 Ligands: R7Y.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.29, A:V.83 Hydrogen bonds: A:M.81, A:V.83, A:R.88, A:R.89, A:Q.90, A:G.91, A:I.92, A:G.93, A:R.94 Water bridges: A:Y.87, A:R.88, A:S.116, A:K.121 Salt bridges: A:R.89 COA.6: 18 residues within 4Å: Chain B: G.28, F.29, M.81, V.82, V.83, R.88, R.89, Q.90, G.91, I.92, G.93, R.94, A.115, S.116, K.121, L.122, Y.123 Ligands: R7Y.5 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.29 Hydrogen bonds: B:M.81, B:V.83, B:R.89, B:Q.90, B:Q.90, B:G.91, B:I.92, B:G.93, B:R.94 Water bridges: B:Y.87, B:R.88, B:R.89, B:R.89, B:L.122 Salt bridges: B:R.89

7 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.4: 2 residues within 4Å: Chain A: E.161, V.162 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.161 Water bridges: A:Q.109, A:D.163 ACT.7: 4 residues within 4Å: Chain B: D.69, D.163, T.165, A.166 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.167 ACT.8: 3 residues within 4Å: Chain B: G.133, R.145, E.150 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.145 ACT.9: 2 residues within 4Å: Chain B: I.147, E.148 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.147 Water bridges: B:E.148 ACT.10: 3 residues within 4Å: Chain B: S.86, Y.87, Q.90 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.90 ACT.11: 2 residues within 4Å: Chain B: L.68, E.161 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bassenden, A.V. et al., Structural and phylogenetic analyses of resistance to next-generation aminoglycosides conferred by AAC(2') enzymes. Sci Rep (2021)

Release Date

2021-06-02

Peptides

Aminoglycoside 2'-N-acetyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aminoglycoside 2'-N-acetyltransferase