SMTL ID : 7ea9.1 (1 other biounit)

Crystal Structure of human lysyl-tRNA synthetase Y145H mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x KAA: 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE(Non-covalent)

KAA.1: 27 residues within 4Å: Chain A: G.209, A.210, A.231, E.233, R.255, E.257, T.262, H.263, N.264, F.267, T.269, E.271, Y.273, E.426, I.427, C.428, N.429, A.430, Y.431, E.433, G.478, W.479, G.480, G.482, R.485, I.496 Ligands: GOL.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.431 Hydrogen bonds: A:R.255, A:E.257, A:E.257, A:N.264, A:E.271, A:E.426, A:E.426, A:N.429, A:E.433, A:G.482, A:R.485 Water bridges: A:Y.431, A:D.484 Salt bridges: A:R.255 pi-Stacking: A:F.267, A:F.267 KAA.3: 26 residues within 4Å: Chain B: G.209, A.210, A.231, E.233, R.255, E.257, T.262, H.263, N.264, F.267, T.269, E.271, Y.273, E.426, I.427, N.429, A.430, Y.431, E.433, G.478, W.479, G.480, G.482, R.485, I.496 Ligands: GOL.4 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Y.431 Hydrogen bonds: B:E.233, B:R.255, B:R.255, B:E.257, B:E.257, B:N.264, B:E.271, B:Y.273, B:E.426, B:E.426, B:N.429, B:E.433, B:G.482, B:R.485 Water bridges: B:V.211 Salt bridges: B:R.255 pi-Stacking: B:F.267, B:F.267 pi-Cation interactions: B:R.485

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: H.263, E.426, R.485 Ligands: KAA.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.263, A:R.485, A:R.485 GOL.4: 6 residues within 4Å: Chain B: R.255, E.257, H.263, E.426, R.485 Ligands: KAA.3 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.255, B:E.257, B:R.485, B:R.485

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, S. et al., Structural analyses of a human lysyl-tRNA synthetase mutant associated with autosomal recessive nonsyndromic hearing impairment. Biochem.Biophys.Res.Commun. (2021)

Release Date

2021-03-31

Peptides

Lysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine--tRNA ligase

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