SMTL ID : 3hxy.1

Crystal Structure of catalytic fragment of E. coli AlaRS in complex with AMPPCP, Ala-AMP and PCP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

monomer

Ligands

1 x 5AL: 5'-O-[(R)-{[(2S)-2-aminopropanoyl]oxy}(hydroxy)phosphoryl]adenosine(Non-covalent)

5AL.1: 21 residues within 4Å: Chain A: A.41, M.43, R.69, D.76, R.85, H.86, H.87, F.90, M.92, W.170, E.209, I.210, N.212, V.214, D.235, T.236, G.237, G.239, R.242 Ligands: ACP.3, MG.4 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.214 Hydrogen bonds: A:R.69, A:D.76, A:H.87, A:W.170, A:N.212, A:D.235, A:G.239, A:R.242, A:R.242, A:R.242 Water bridges: A:G.42, A:N.253 Salt bridges: A:R.69, A:R.69 pi-Stacking: A:F.90, A:F.90 pi-Cation interactions: A:R.242

1 x MDN: METHYLENEDIPHOSPHONIC ACID(Non-covalent)

MDN.2: 10 residues within 4Å: Chain A: R.85, H.86, D.167, E.209, R.242 Ligands: ACP.3, MG.4, MG.5, MG.6, MG.7 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.85, A:D.167, A:R.242, A:R.242 Water bridges: A:R.85, A:D.167, A:D.203, A:E.209, A:E.209, A:E.209

1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.3: 21 residues within 4Å: Chain A: R.69, D.76, R.85, H.86, H.87, F.90, M.92, W.170, E.209, I.210, W.211, N.212, G.237, G.239, R.242 Ligands: 5AL.1, MDN.2, MG.4, MG.5, MG.6, MG.7 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:R.69, A:D.76, A:H.87, A:E.209, A:N.212, A:N.212, A:G.239, A:R.242, A:R.242 Water bridges: A:R.85, A:R.85, A:E.209, A:E.209, A:E.209, A:N.253 Salt bridges: A:R.69 pi-Stacking: A:F.90, A:F.90 pi-Cation interactions: A:R.242, A:R.242

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

MG.4: 8 residues within 4Å: Chain A: E.183, E.209, N.212 Ligands: 5AL.1, MDN.2, ACP.3, MG.6, MG.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.183, A:E.209, H2O.14 MG.5: 2 residues within 4Å: Ligands: MDN.2, ACP.3 No protein-ligand interaction detected (PLIP) MG.6: 7 residues within 4Å: Chain A: D.167, E.183, E.209 Ligands: MDN.2, ACP.3, MG.4, MG.7 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.183, A:E.183, A:E.209, H2O.5 MG.7: 7 residues within 4Å: Chain A: D.167, E.183, E.209 Ligands: MDN.2, ACP.3, MG.4, MG.6 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.209, H2O.5

1 x HED: 2-HYDROXYETHYL DISULFIDE(Non-covalent)

HED.8: 6 residues within 4Å: Chain A: K.2, A.10, K.118, W.119, F.120, L.247 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.2, A:K.2, A:L.247 Water bridges: A:K.118

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, M. et al., Paradox of mistranslation of serine for alanine caused by AlaRS recognition dilemma. Nature (2009)

Release Date

2009-12-15

Peptides

Alanyl-tRNA synthetase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alanyl-tRNA synthetase

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