SMTL ID : 6chd.1

Crystal Structure of Human Lysyl-tRNA Synthetase complexed with L-Lysylsulfamoyl Adenosine

Coordinates

PDB Format

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: 25 residues within 4Å: Chain A: G.277, A.278, A.299, E.301, R.323, E.325, T.330, H.331, N.332, F.335, T.337, E.339, Y.341, E.494, I.495, C.496, N.497, Y.499, E.501, G.546, W.547, G.548, G.550, R.553, I.564 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.499 Hydrogen bonds: A:R.323, A:R.323, A:E.325, A:E.325, A:N.332, A:E.339, A:E.494, A:N.497, A:E.501, A:G.550, A:R.553 Water bridges: A:Y.499, A:D.552 Salt bridges: A:R.323 pi-Stacking: A:F.335, A:F.335 pi-Cation interactions: A:R.553 KAA.9: 25 residues within 4Å: Chain B: G.277, A.278, A.299, E.301, R.323, E.325, T.330, H.331, N.332, F.335, T.337, E.339, Y.341, E.494, I.495, C.496, N.497, Y.499, E.501, G.546, W.547, G.548, G.550, R.553, I.564 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:Y.499 Hydrogen bonds: B:E.301, B:R.323, B:R.323, B:E.325, B:E.325, B:N.332, B:E.339, B:Y.341, B:Y.341, B:E.494, B:E.494, B:N.497, B:G.550, B:R.553 Water bridges: B:Y.499 Salt bridges: B:R.323 pi-Stacking: B:F.335, B:F.335 pi-Cation interactions: B:R.553

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

SO4.2: 3 residues within 4Å: Chain A: P.435, R.442, K.446 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.442, A:K.446 SO4.3: 2 residues within 4Å: Chain A: H.133, R.148 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.133, A:R.148 SO4.4: 4 residues within 4Å: Chain A: K.363, G.367, S.368, Y.369 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.368, A:Y.369 Salt bridges: A:K.363 SO4.5: 3 residues within 4Å: Chain A: A.382, Y.383, D.384 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.384, A:D.384 SO4.6: 2 residues within 4Å: Chain A: G.377, N.562 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.562 Water bridges: A:N.562, A:N.563 SO4.7: 2 residues within 4Å: Chain A: I.170, N.174 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.174, A:N.174 SO4.11: 3 residues within 4Å: Chain B: H.331, E.494, R.553 4 PLIP interactions: 4 interactions with chain B Water bridges: B:E.494, B:R.553 Salt bridges: B:H.331, B:R.553 SO4.12: 3 residues within 4Å: Chain B: P.435, R.442, K.446 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.442, B:K.446 SO4.13: 3 residues within 4Å: Chain B: Y.253, S.256, F.257 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.256 SO4.14: 2 residues within 4Å: Chain B: K.363, H.364 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.363, B:H.364 SO4.15: 2 residues within 4Å: Chain B: H.120, N.162 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.162 Salt bridges: B:H.120

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

EDO.8: 3 residues within 4Å: Chain A: F.144, T.191, K.192 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.192

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 1 residues within 4Å: Chain B: D.123 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dranow, D.M. et al., Crystal Structure of Human Lysyl-tRNA Synthetase complexed with L-Lysylsulfamoyl Adenosine. to be published

Release Date

2018-03-07

Peptides

Lysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine--tRNA ligase