SMTL ID : 5cfu.1

Crystal Structure of ANT(2")-Ia in complex with adenylyl-2"-tobramycin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: D.52, D.54 Ligands: 51H.3, POP.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.52, A:D.54, H2O.2 MN.2: 4 residues within 4Å: Chain A: H.156 Ligands: 51H.3, POP.4, POP.5 No protein-ligand interaction detected (PLIP)

1 x 51H: adenylyl-2"-tobramycin(Non-covalent)

51H.3: 17 residues within 4Å: Chain A: D.52, D.54, Y.82, D.94, E.96, I.107, A.108, D.139, Y.140, Y.142, Y.143, E.146, H.156 Ligands: MN.1, MN.2, POP.4, POP.5 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:D.52, A:D.94, A:E.96, A:D.139 Water bridges: A:Y.82, A:D.94, A:D.94, A:Y.143, A:Y.143, A:Y.143, A:Y.143, A:E.146, A:E.146, A:E.146, A:E.146 Salt bridges: A:H.156 pi-Stacking: A:Y.143, A:Y.143, A:H.156

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.4: 12 residues within 4Å: Chain A: G.36, R.48, H.50, D.51, D.52, D.54, K.155, H.156 Ligands: MN.1, MN.2, 51H.3, POP.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.36, A:D.51, A:D.52 Water bridges: A:S.159 Salt bridges: A:R.48, A:R.48, A:H.50, A:K.155, A:H.156, A:H.156 POP.5: 5 residues within 4Å: Chain A: D.51, K.155 Ligands: MN.2, 51H.3, POP.4 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.143 Salt bridges: A:K.155

3 x BU1: 1,4-BUTANEDIOL(Non-functional Binders)

BU1.6: 3 residues within 4Å: Chain A: P.111, K.171, L.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.171 BU1.7: 1 residues within 4Å: Chain A: W.100 No protein-ligand interaction detected (PLIP) BU1.8: 5 residues within 4Å: Chain A: W.32, A.104, Y.105, C.115, E.117 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.117 Hydrogen bonds: A:Y.105, A:Y.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bassenden, A.V. et al., Revisiting the Catalytic Cycle and Kinetic Mechanism of AminoglycosideO-Nucleotidyltransferase(2′′): A Structural and Kinetic Study. Acs Chem.Biol. (2020)

Release Date

2016-07-20

Peptides

Aminoglycoside Nucleotidyltransferase (2")-Ia: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aminoglycoside Nucleotidyltransferase (2")-Ia

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