SMTL ID : 7mqk.1

AAC(3)-IIIa in complex with CoA and sisomicin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x SIS: (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside(Non-covalent)

SIS.1: 11 residues within 4Å: Chain A: Y.67, I.73, D.75, E.126, Y.149, D.173, H.179, T.215, G.216, F.224 Ligands: COA.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:E.126, A:E.126, A:E.126, A:H.179, A:T.215 Water bridges: A:Y.67, A:D.75, A:D.75, A:D.214, A:G.216, A:G.216, A:G.216, A:G.216, A:G.216, A:G.216 Salt bridges: A:H.179 SIS.3: 11 residues within 4Å: Chain B: Y.67, I.73, D.75, E.126, Y.149, D.173, H.179, T.215, G.216, F.224 Ligands: COA.4 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.67 Hydrogen bonds: B:Y.67, B:E.126, B:E.126, B:H.179, B:T.215 Water bridges: B:D.75, B:D.75, B:E.105, B:G.216, B:G.216, B:G.216, B:G.216, B:G.216, B:G.216 Salt bridges: B:H.179 SIS.6: 11 residues within 4Å: Chain C: Y.67, I.73, D.75, E.126, Y.149, D.173, H.179, T.215, G.216, F.224 Ligands: COA.7 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:Y.67, C:E.126, C:E.126, C:H.179, C:T.215 Water bridges: C:D.75, C:D.75, C:D.75, C:E.105, C:D.173, C:G.216, C:G.216, C:G.216, C:G.216, C:G.216, C:G.216 SIS.8: 11 residues within 4Å: Chain D: Y.67, I.73, D.75, E.126, Y.149, D.173, H.179, T.215, G.216, F.224 Ligands: COA.9 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:E.126, D:E.126, D:E.126, D:H.179, D:T.215 Water bridges: D:Y.67, D:D.75, D:D.75, D:D.75, D:D.75, D:E.105, D:E.105, D:D.173, D:D.214, D:G.216, D:G.216

4 x COA: COENZYME A(Non-covalent)

COA.2: 17 residues within 4Å: Chain A: H.34, A.35, S.36, V.37, K.38, P.47, Y.67, E.105, N.106, S.107, V.108, F.112, A.170, P.171, T.174, T.176 Ligands: SIS.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.35, A:V.37, A:K.38, A:E.105, A:S.107, A:V.108 Salt bridges: A:K.38 COA.4: 17 residues within 4Å: Chain B: H.34, A.35, S.36, V.37, K.38, P.47, Y.67, E.105, N.106, S.107, V.108, F.112, A.170, P.171, T.174, T.176 Ligands: SIS.3 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:H.34, B:A.35, B:V.37, B:K.38, B:E.105, B:S.107, B:V.108 Water bridges: B:A.35, B:S.36 Salt bridges: B:K.38 COA.7: 17 residues within 4Å: Chain C: H.34, A.35, S.36, V.37, K.38, P.47, Y.67, E.105, N.106, S.107, V.108, F.112, A.170, P.171, T.174, T.176 Ligands: SIS.6 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:H.34, C:A.35, C:V.37, C:K.38, C:E.105, C:S.107, C:V.108 Water bridges: C:S.36, C:K.38, C:K.38 Salt bridges: C:K.38 COA.9: 17 residues within 4Å: Chain D: H.34, A.35, S.36, V.37, K.38, P.47, Y.67, E.105, N.106, S.107, V.108, F.112, A.170, P.171, T.174, T.176 Ligands: SIS.8 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:A.35, D:V.37, D:K.38, D:E.105, D:S.107, D:V.108 Salt bridges: D:K.38

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain B: L.89, P.196, W.207, V.208, T.209 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.207, B:T.209 Water bridges: B:T.209

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zielinski, M. et al., Structural elucidation of substrate-bound aminoglycoside acetyltransferase (3)-IIIa. Plos One (2022)

Release Date

2022-07-06

Peptides

Aminoglycoside N(3)-acetyltransferase III: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Aminoglycoside N(3)-acetyltransferase III

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