SMTL ID : 7mql.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x COA: COENZYME A(Non-covalent)

COA.1: 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: RIO.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:A.35, A:V.37, A:K.38, A:E.105, A:S.107, A:V.108 Water bridges: A:A.35, A:S.36, A:K.38, A:K.38 Salt bridges: A:K.38 COA.5: 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: RIO.6 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:H.34, B:A.35, B:V.37, B:K.38, B:K.38, B:E.105, B:S.107, B:V.108 Water bridges: B:S.36 Salt bridges: B:K.38 COA.9: 18 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: FMT.10, RIO.11 9 PLIP interactions: 9 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:A.35 Salt bridges: C:K.38 COA.14: 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: RIO.15 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:A.35, D:V.37, D:K.38, D:E.105, D:S.107, D:V.108 Water bridges: D:A.35, D:S.36 Salt bridges: D:K.38

4 x RIO: RIBOSTAMYCIN(Non-covalent)

RIO.2: 10 residues within 4Å: Chain A: Y.67, E.126, Y.149, D.173, T.174, H.179, T.215, G.216, F.224 Ligands: COA.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.126, A:Y.149, A:D.173, A:H.179 Water bridges: A:E.126, A:T.215 Salt bridges: A:H.179 RIO.6: 10 residues within 4Å: Chain B: Y.67, E.126, Y.149, D.173, T.174, H.179, T.215, G.216, F.224 Ligands: COA.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.67, B:D.173, B:D.173, B:T.215, B:T.215 RIO.11: 10 residues within 4Å: Chain C: Y.67, E.126, Y.149, D.173, T.174, H.179, T.215, G.216, F.224 Ligands: COA.9 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Y.67, C:D.173, C:D.173, C:T.215, C:T.215 Water bridges: C:D.173, C:T.215 RIO.15: 10 residues within 4Å: Chain D: Y.67, E.126, Y.149, D.173, T.174, H.179, T.215, G.216, F.224 Ligands: COA.14 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:Y.67 Hydrogen bonds: D:E.126, D:Y.149, D:D.173, D:D.173, D:T.215, D:T.215 Water bridges: D:Y.67

8 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 5 residues within 4Å: Chain A: H.15, A.19, K.241, V.242, G.243 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.15, A:G.243 FMT.4: 3 residues within 4Å: Chain A: Y.147, Y.183, Y.213 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.183, A:Y.183 Water bridges: A:Y.213 FMT.7: 6 residues within 4Å: Chain B: H.11, H.15, L.16, A.19, V.242, G.243 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.243 Water bridges: B:A.19 FMT.8: 5 residues within 4Å: Chain B: Q.135, L.138 Chain C: K.157, A.160, I.161 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.135 Water bridges: B:L.138 FMT.10: 3 residues within 4Å: Chain C: R.104, V.108 Ligands: COA.9 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.104 Water bridges: C:R.104 FMT.12: 6 residues within 4Å: Chain A: L.138, K.157, I.161 Chain D: A.141, N.142, K.157 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.142 Water bridges: D:A.141, D:K.157 FMT.13: 5 residues within 4Å: Chain C: S.79, L.80, P.81 Chain D: R.188, H.189 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.188, D:R.188 FMT.16: 2 residues within 4Å: Chain D: L.84, Y.88 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.88, D:Y.88

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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