SMTL ID : 5f49.3 (2 other biounits)

Crystal structure of an aminoglycoside acetyltransferase meta-AAC0020 from an uncultured soil metagenomic sample in complex with malonyl-coenzyme A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-tetramer

Ligands

1 x COA: COENZYME A(Non-covalent)

COA.1: 22 residues within 4Å: Chain A: V.34, F.35, L.92, A.93, V.94, Q.99, R.100, Q.101, G.102, I.103, G.104, K.105, Q.126, A.127, D.131, Y.133, A.134, D.136, F.137, Y.138, S.140 Ligands: MG.4 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:V.34, A:F.35, A:L.92 Hydrogen bonds: A:L.92, A:V.94, A:Q.99, A:R.100, A:R.100, A:G.102, A:I.103, A:G.104, A:K.105, A:S.140 Water bridges: A:L.92, A:R.100, A:Q.101, A:Q.101, A:D.136 Salt bridges: A:R.100 pi-Cation interactions: A:R.100, A:R.100

8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 3 residues within 4Å: Chain A: E.18, N.53, N.55 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.18, A:N.53, H2O.4, H2O.4, H2O.4 MG.3: 1 residues within 4Å: Chain A: N.39 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: COA.1 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: E.14, D.20 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.14, B:D.20, B:D.20, H2O.7, H2O.8 MG.7: 3 residues within 4Å: Chain A: D.44 Chain B: E.83 Chain C: F.40 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: C:F.40, B:E.83, H2O.1, H2O.2, H2O.7 MG.9: 1 residues within 4Å: Ligands: MLC.8 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain D: E.14, D.20 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.14, D:D.20, H2O.15, H2O.15, H2O.16 MG.12: 3 residues within 4Å: Chain A: F.40 Chain C: D.44 Chain D: E.83 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: A:F.40, D:E.83, H2O.11, H2O.12, H2O.14

3 x MLC: MALONYL-COENZYME A(Non-covalent)

MLC.5: 19 residues within 4Å: Chain B: V.34, F.35, D.91, L.92, A.93, V.94, Q.99, R.100, Q.101, G.102, I.103, G.104, K.105, D.128, Y.133, D.136, F.137, Y.138, S.140 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.35, B:L.92, B:V.94 Hydrogen bonds: B:D.91, B:V.94, B:R.100, B:G.102, B:I.103, B:G.104, B:K.105, B:D.131, B:D.136, B:S.140 Water bridges: B:Q.99, B:Q.101, B:A.134 Salt bridges: B:K.105 MLC.8: 21 residues within 4Å: Chain C: V.34, F.35, Y.90, D.91, L.92, A.93, V.94, Q.99, R.100, Q.101, G.102, I.103, G.104, K.105, Q.126, Y.133, D.136, F.137, Y.138, S.140 Ligands: MG.9 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:V.34, C:F.35, C:L.92, C:Y.133 Hydrogen bonds: C:D.91, C:L.92, C:L.92, C:V.94, C:R.100, C:R.100, C:Q.101, C:G.102, C:G.102, C:I.103, C:G.104, C:K.105, C:Q.126, C:S.140, C:S.140 Salt bridges: C:R.100 pi-Cation interactions: C:R.100 MLC.10: 22 residues within 4Å: Chain D: V.34, F.35, Y.90, D.91, L.92, A.93, V.94, Q.99, R.100, Q.101, G.102, I.103, G.104, K.105, Q.126, D.131, Y.133, A.134, D.136, F.137, Y.138, S.140 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:F.35, D:L.92 Hydrogen bonds: D:L.92, D:L.92, D:L.92, D:R.100, D:G.102, D:G.102, D:I.103, D:G.104, D:K.105, D:Q.126, D:Y.133, D:D.136, D:S.140 Water bridges: D:Y.88 Salt bridges: D:R.100, D:K.105 pi-Cation interactions: D:R.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Z. et al., Structural and Functional Survey of Environmental Aminoglycoside Acetyltransferases Reveals Functionality of Resistance Enzymes. ACS Infect Dis (2017)

Release Date

2015-12-16

Peptides

aminoglycoside acetyltransferase meta-AAC0020: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

aminoglycoside acetyltransferase meta-AAC0020

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