SMTL ID : 6blj.1 (2 other biounits)

Crystal structure of cytoplasmic Serine-tRNA ligase from Naegleria fowleri in complex with AMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 14 residues within 4Å: Chain A: R.314, E.316, F.328, R.329, V.330, F.333, K.335, E.406, L.407, V.408, S.409, T.444, A.447, R.450 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:E.316, A:V.330, A:L.407, A:S.409, A:R.450 Water bridges: A:R.314, A:R.329, A:A.447, A:R.450 Salt bridges: A:R.314 pi-Stacking: A:F.333 pi-Cation interactions: A:R.450, A:R.450 AMP.3: 14 residues within 4Å: Chain B: R.314, E.316, F.328, R.329, V.330, F.333, K.335, E.406, L.407, V.408, S.409, T.444, A.447, R.450 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:E.316, B:V.330, B:E.406, B:L.407, B:S.409, B:R.450 Water bridges: B:T.283, B:R.314, B:R.329, B:A.447, B:R.450 Salt bridges: B:R.314 pi-Stacking: B:F.333 pi-Cation interactions: B:R.450, B:R.450 AMP.5: 14 residues within 4Å: Chain C: R.314, E.316, F.328, R.329, V.330, F.333, K.335, E.406, L.407, V.408, S.409, T.444, A.447, R.450 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:E.316, C:V.330, C:E.406, C:L.407, C:S.409, C:R.450 Water bridges: C:R.314, C:R.314, C:R.314, C:R.314, C:S.409, C:T.444, C:A.447 Salt bridges: C:R.314 pi-Stacking: C:F.333 pi-Cation interactions: C:R.450, C:R.450 AMP.7: 14 residues within 4Å: Chain D: R.314, E.316, F.328, R.329, V.330, F.333, K.335, E.406, L.407, V.408, S.409, T.444, A.447, R.450 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:E.316, D:V.330, D:E.406, D:E.406, D:L.407, D:S.409, D:R.450 Water bridges: D:R.314, D:R.329, D:R.450, D:T.451 Salt bridges: D:R.314 pi-Stacking: D:F.333 pi-Cation interactions: D:R.450, D:R.450

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: H.155, W.350, F.353, D.354, K.387 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.387 EDO.4: 6 residues within 4Å: Chain B: H.155, T.157, W.350, F.353, D.354, K.387 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.354 Water bridges: B:H.155 EDO.6: 4 residues within 4Å: Chain C: W.350, F.353, D.354, K.387 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.387, C:K.387 EDO.8: 6 residues within 4Å: Chain D: H.155, T.157, W.350, F.353, D.354, K.387 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.354 Water bridges: D:H.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of cytoplasmic Serine-tRNA ligase from Neisseria fowlerii in complex with AMP. TO BE PUBLISHED

Release Date

2017-12-20

Peptides

Serine-tRNA ligase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
B

Serine-tRNA ligase

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