SMTL ID : 3r78.1 (5 other biounits)

Crystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, ATP-bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 20 residues within 4Å: Chain A: D.52, V.54, G.55, Q.56, S.57, I.61, F.74, K.76, P.103, T.119, T.120, A.121, I.122, D.223, N.224, I.226, I.236, D.237 Ligands: CA.2, CA.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Q.56, A:S.57, A:S.57, A:T.119, A:T.120, A:I.122 Water bridges: A:A.59, A:A.59, A:R.63, A:K.76, A:K.76, A:D.223 Salt bridges: A:K.76, A:K.76 pi-Stacking: A:F.74, A:F.74

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: N.224, D.237 Ligands: ATP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.237, H2O.15 CA.3: 2 residues within 4Å: Chain A: D.237 Ligands: ATP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.237, A:D.237, H2O.14, H2O.76 CA.13: 1 residues within 4Å: Chain A: D.52 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.52, H2O.8, H2O.9, H2O.16, H2O.21 CA.14: 3 residues within 4Å: Chain A: D.186, D.188, E.290 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.186, A:D.188, H2O.58, H2O.59

9 x NA: SODIUM ION(Non-functional Binders)

NA.4: 1 residues within 4Å: Chain A: E.132 No protein-ligand interaction detected (PLIP) NA.5: 1 residues within 4Å: Chain A: N.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.140 NA.6: 1 residues within 4Å: Chain A: W.200 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.200 NA.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.8: 1 residues within 4Å: Chain A: E.197 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.197 NA.9: 2 residues within 4Å: Chain A: N.94, I.105 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.94 Water bridges: A:I.105 NA.10: 2 residues within 4Å: Chain A: D.189, N.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.189, A:N.192 NA.11: 2 residues within 4Å: Chain A: N.163, D.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.163, A:D.165 NA.12: 3 residues within 4Å: Chain A: N.37, N.39, I.109 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.37, A:N.39

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain A: D.189 Ligand excluded by PLIP CL.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

2 x PE3: 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL(Non-functional Binders)

PE3.18: 5 residues within 4Å: Chain A: D.186, D.219, R.240, D.289, F.292 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.219 PE3.19: 5 residues within 4Å: Chain A: R.150, R.246, Y.272, G.273, I.274 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.246 Water bridges: A:R.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stogios, P.J. et al., Crystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, ATP-bound. TO BE PUBLISHED

Release Date

2011-04-13

Peptides

Aminoglycoside 3'-phosphotransferase AphA1-IAB: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aminoglycoside 3'-phosphotransferase AphA1-IAB

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