SMTL ID : 3w0s.1

Crystal structure of aminoglycoside phosphotransferase APH(4)-Ia, ternary complex with AMP-PNP and hygromycin B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

monomer

Ligands

1 x HY0: HYGROMYCIN B VARIANT(Non-covalent)

HY0.1: 17 residues within 4Å: Chain A: Q.101, D.198, F.199, S.201, N.202, D.216, S.218, E.219, N.231, W.235, W.238, L.239, M.242, Q.273, D.285 Ligands: ANP.2, MG.4 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:Q.101, A:Q.101, A:D.198, A:D.198, A:S.201, A:S.201, A:N.202, A:N.202, A:N.231, A:Q.273, A:D.285 Water bridges: A:N.203, A:N.203, A:D.216, A:Q.273, A:D.280, A:D.285, A:D.285

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 14 residues within 4Å: Chain A: L.28, S.29, A.36, V.47, P.75, R.93, R.94, A.95, N.202, N.203, L.205, I.215 Ligands: HY0.1, MG.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.29, A:S.92, A:S.92, A:A.95, A:N.202, A:N.202, A:N.202 Water bridges: A:S.34, A:S.34, A:D.216, A:D.216

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

MG.3: 1 residues within 4Å: Ligands: ANP.2 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: N.202 Ligands: HY0.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Iino, D. et al., Crystal structures of the ternary complex of APH(4)-Ia/Hph with hygromycin B and an ATP analog using a thermostable mutant. J.Struct.Biol. (2013)

Release Date

2013-08-07

Peptides

Hygromycin-B 4-O-kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Hygromycin-B 4-O-kinase