SMTL ID : 4xeo.1 (1 other biounit)

Crystal Structure of human AlaRS catalytic domain with R329H mutation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

monomer

Ligands

1 x A5A: '5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE(Non-covalent)

A5A.1: 19 residues within 4Å: Chain A: A.64, M.66, R.97, Y.113, H.114, H.115, F.118, M.120, W.196, E.233, I.234, W.235, N.236, V.238, D.259, T.260, G.261, G.263, R.266 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.238 Hydrogen bonds: A:R.97, A:R.97, A:H.115, A:H.115, A:E.233, A:N.236, A:N.236, A:D.259, A:G.261, A:G.263, A:R.266 Water bridges: A:E.209, A:N.277 Salt bridges: A:R.97 pi-Stacking: A:F.118, A:F.118 pi-Cation interactions: A:R.266

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: H.47, S.48, S.49, A.50, K.94, E.383 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.49, A:K.94, A:E.383 Water bridges: A:S.48 GOL.3: 4 residues within 4Å: Chain A: Q.32, I.35, K.39, Y.45 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.32, A:Q.32, A:K.39 Water bridges: A:Q.32, A:K.39, A:A.380

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 5 residues within 4Å: Chain A: Y.129, F.130, K.131, E.132, L.133 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.130, A:E.132, A:L.133 Water bridges: A:D.128, A:K.131 SO4.5: 4 residues within 4Å: Chain A: D.106, R.350, R.353, Y.354 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.354 Salt bridges: A:R.350, A:R.353

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain A: E.209, E.233 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.209, A:E.233, H2O.8, H2O.9, H2O.11, H2O.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, X.L., Crystal structure of human AlaRS catalytic domain with R329H mutation. To Be Published

Release Date

2015-12-30

Peptides

Alanine--tRNA ligase, cytoplasmic: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Alanine--tRNA ligase, cytoplasmic

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