SMTL ID : 2j3m.1

PROLYL-TRNA SYNTHETASE FROM ENTEROCOCCUS FAECALIS COMPLEXED WITH ATP, manganese and prolinol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

ATP.1: 21 residues within 4Å: Chain A: R.140, E.142, L.149, L.150, R.151, G.152, F.155, M.157, E.407, I.408, G.409, H.410, F.412, G.442, I.443, G.444, R.447 Ligands: PRI.2, MN.3, MN.4, MN.10 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:E.142, A:R.151, A:G.152, A:E.407, A:E.407, A:G.444, A:R.447 Water bridges: A:R.140, A:R.140, A:D.219 Salt bridges: A:R.140, A:R.140, A:R.151, A:R.447 pi-Stacking: A:F.155, A:F.155 pi-Cation interactions: A:R.447, A:R.447 ATP.5: 20 residues within 4Å: Chain B: R.140, E.142, L.149, L.150, R.151, G.152, F.155, M.157, D.219, E.407, I.408, G.409, H.410, G.442, G.444, R.447 Ligands: PRI.6, MN.7, MN.8, MN.9 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:R.140, B:E.142, B:E.142, B:G.152, B:E.407, B:E.407, B:G.444, B:R.447 Water bridges: B:R.151, B:R.151, B:R.151, B:D.219 Salt bridges: B:R.140, B:R.140, B:R.151, B:R.447 pi-Stacking: B:F.155, B:F.155 pi-Cation interactions: B:R.447, B:R.447

2 x PRI: PYRROLIDINE-2-CARBALDEHYDE(Non-covalent)

PRI.2: 11 residues within 4Å: Chain A: T.109, E.111, R.140, M.157, D.159, Y.161, F.412, C.440, Y.441, G.442 Ligands: ATP.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.159, A:F.412 Hydrogen bonds: A:T.109, A:R.140 Water bridges: A:R.85 PRI.6: 10 residues within 4Å: Chain B: T.109, E.111, R.140, M.157, D.159, Y.161, C.440, Y.441, G.442 Ligands: ATP.5 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:D.159 Hydrogen bonds: B:T.109, B:R.140, B:Y.161 Water bridges: B:R.85, B:R.85

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

MN.3: 5 residues within 4Å: Chain A: E.407, H.410, F.412 Ligands: ATP.1, MN.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.407, A:H.410, H2O.8 MN.4: 4 residues within 4Å: Chain A: E.209, E.407 Ligands: ATP.1, MN.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.407, H2O.8 MN.7: 4 residues within 4Å: Chain B: E.407, H.410 Ligands: ATP.5, MN.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.407, B:H.410, H2O.14 MN.8: 4 residues within 4Å: Chain B: E.209, E.407 Ligands: ATP.5, MN.7 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.407, H2O.14 MN.9: 4 residues within 4Å: Chain B: R.140, E.142, R.151 Ligands: ATP.5 No protein-ligand interaction detected (PLIP) MN.10: 2 residues within 4Å: Chain A: R.151 Ligands: ATP.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crepin, T. et al., Structures of Two Bacterial Prolyl-tRNA Synthetases with and without a Cis-Editing Domain. Structure (2006)

Release Date

2006-10-11

Peptides

PROLYL-TRNA SYNTHETASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PROLYL-TRNA SYNTHETASE

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