SMTL ID : 5vl1.5 (5 other biounits)

Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulcerans complexed with L-lysine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 11 residues within 4Å: Chain A: T.270, H.271, S.272, F.275, E.423, L.424, A.425, T.426, G.477, G.479, R.482 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.272, A:G.479, A:R.482 PGE.5: 12 residues within 4Å: Chain B: T.270, H.271, S.272, F.275, E.423, L.424, A.425, T.426, G.477, G.479, R.482 Ligands: LYS.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.270, B:S.272, B:E.423, B:G.479, B:R.482

2 x LYS: LYSINE(Non-covalent)

LYS.2: 14 residues within 4Å: Chain A: G.217, A.218, A.239, E.241, R.263, M.277, E.279, Y.281, T.426, Y.428, E.430, G.475, T.476, G.477 9 PLIP interactions: 1 Ligand-Ligand interactions, 8 interactions with chain A Hydrogen bonds: K.2, A:G.217, A:E.241, A:E.279, A:E.279, A:Y.281, A:E.430 Hydrophobic interactions: A:T.426 Salt bridges: A:R.263 LYS.6: 15 residues within 4Å: Chain B: G.217, A.218, A.239, E.241, R.263, M.277, E.279, Y.281, T.426, Y.428, E.430, G.475, T.476, G.477 Ligands: PGE.5 4 PLIP interactions: 4 interactions with chain B, Hydrophobic interactions: B:T.426 Hydrogen bonds: B:G.217, B:E.430 Salt bridges: B:R.263

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 3 residues within 4Å: Chain A: P.17, E.18, Q.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.18, A:Q.19 PEG.4: 6 residues within 4Å: Chain A: R.403, Q.404, H.405, R.406, S.407 Chain B: D.36 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.36, A:R.403, A:R.403, A:Q.404, A:S.407 PEG.7: 2 residues within 4Å: Chain B: E.33, Y.35 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dranow, D.M. et al., Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulcerans complexed with L-lysine. to be published

Release Date

2017-05-10

Peptides

Lysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine--tRNA ligase

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