SMTL ID : 6wbd.1

Crystal Structure of Lysyl-tRNA synthetase from Stenotrophomonas maltophilia with bound L-lysine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 13 residues within 4Å: Chain A: G.223, A.224, A.245, E.247, E.285, Y.287, N.431, G.432, F.433, E.435, G.480, L.481, G.482 8 PLIP interactions: 8 interactions with chain A, Hydrophobic interactions: A:F.433 Hydrogen bonds: A:G.223, A:E.247, A:E.285, A:Y.287, A:N.431, A:E.435 Water bridges: A:N.267 LYS.31: 12 residues within 4Å: Chain B: G.223, A.224, A.245, E.247, E.285, Y.287, N.431, F.433, E.435, G.480, L.481, G.482 5 PLIP interactions: 5 interactions with chain B, Hydrophobic interactions: B:F.433 Hydrogen bonds: B:G.223, B:N.431, B:N.431, B:E.435

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

EDO.2: 9 residues within 4Å: Chain A: T.254, V.255, G.257, E.259, Y.290, M.475, A.476 Chain B: R.81, I.127 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: P.439, E.440, A.443, I.468, E.472 Chain B: R.28 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: D.205, F.209, L.210, E.211 Chain B: S.194, R.198 Ligands: EDO.15 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: Y.293, N.294, M.297, T.397, D.398 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: Y.249, R.252, D.466 Chain B: R.174, Y.177, F.504 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: M.283, E.428, L.429, A.430, N.431, G.482, G.484 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: R.266, L.502 Chain B: E.213, P.215 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: H.342, T.385, H.388, T.389 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: M.83, V.124, P.160 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: A.115, S.148, I.149 Ligands: EDO.19, EDO.22 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: A.199, A.202, W.203, D.306, A.310 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: L.23, E.26, R.27, K.30, D.123 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: A.188, V.189, K.192, T.493 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: D.205, F.209 Ligands: EDO.4 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: R.408, D.438, D.441 Chain B: Y.41 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: R.276, H.277, R.487, M.490, I.498 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: N.312, G.314, T.315, E.316 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain A: F.45, A.129, E.131, S.148, I.149, R.150 Ligands: EDO.11 Ligand excluded by PLIP EDO.20: 8 residues within 4Å: Chain A: P.215, M.217, H.218, Y.219, Y.249 Chain B: F.504, P.505, Y.506 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain A: D.438, D.441, Q.444 Chain B: R.35 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: V.111, L.112, A.115, E.147 Ligands: EDO.11 Ligand excluded by PLIP EDO.23: 1 residues within 4Å: Chain A: R.332 Ligand excluded by PLIP EDO.24: 10 residues within 4Å: Chain A: R.201, E.211, I.264, N.265 Chain B: R.201, E.211, I.264, N.265 Ligands: EDO.25, EDO.38 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain A: R.201, I.264, N.265 Chain B: E.211, E.213 Ligands: EDO.24 Ligand excluded by PLIP EDO.26: 8 residues within 4Å: Chain A: S.194, K.195, R.198 Chain B: D.205, F.209, L.210, E.211 Ligands: EDO.45 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain A: E.440 Chain B: R.28, L.31, K.32, R.35 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain A: R.28, L.31, K.32, R.35 Chain B: E.440 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain A: E.213, P.215 Chain B: R.266, L.502, F.504 Ligand excluded by PLIP EDO.32: 8 residues within 4Å: Chain A: R.81, I.127 Chain B: T.254, V.255, G.257, E.259, M.475, A.476 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain A: R.28 Chain B: P.439, E.440, A.443, I.468, E.472 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain A: R.157 Chain B: Y.463, A.465, I.468, E.472 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain B: Y.293, N.294, R.332, T.397 Ligands: EDO.40, EDO.51 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain A: R.174, Y.177, F.504 Chain B: Y.249, R.252, D.466 Ligand excluded by PLIP EDO.37: 6 residues within 4Å: Chain B: M.283, E.428, L.429, A.430, N.431, G.484 Ligand excluded by PLIP EDO.38: 6 residues within 4Å: Chain A: E.211, E.213 Chain B: R.201, I.264, N.265 Ligands: EDO.24 Ligand excluded by PLIP EDO.39: 6 residues within 4Å: Chain B: F.93, Q.104, T.137, T.139, E.141 Ligands: EDO.49 Ligand excluded by PLIP EDO.40: 5 residues within 4Å: Chain B: Y.293, N.294, N.410, D.418 Ligands: EDO.35 Ligand excluded by PLIP EDO.41: 2 residues within 4Å: Chain B: M.83, P.160 Ligand excluded by PLIP EDO.42: 3 residues within 4Å: Chain B: A.199, W.203, D.306 Ligand excluded by PLIP EDO.43: 4 residues within 4Å: Chain B: A.188, V.189, K.192, T.493 Ligand excluded by PLIP EDO.44: 8 residues within 4Å: Chain B: P.221, A.224, A.226, P.228, V.244, E.459, A.460, M.461 Ligand excluded by PLIP EDO.45: 6 residues within 4Å: Chain A: K.195 Chain B: D.205, D.208, F.209, L.210 Ligands: EDO.26 Ligand excluded by PLIP EDO.46: 2 residues within 4Å: Chain B: G.314, T.315 Ligand excluded by PLIP EDO.47: 5 residues within 4Å: Chain B: R.269, R.276, H.277, R.487, M.490 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain B: F.45, E.131, S.148, I.149, R.150 Ligand excluded by PLIP EDO.49: 7 residues within 4Å: Chain B: A.84, R.86, F.93, A.94, Q.95, Q.104 Ligands: EDO.39 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain A: R.35 Chain B: D.438, E.440, D.441, Q.444 Ligand excluded by PLIP EDO.51: 2 residues within 4Å: Chain B: R.332 Ligands: EDO.35 Ligand excluded by PLIP EDO.52: 4 residues within 4Å: Chain B: N.294, E.295, D.298, R.332 Ligand excluded by PLIP EDO.53: 1 residues within 4Å: Chain B: A.384 Ligand excluded by PLIP

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.28: 3 residues within 4Å: Chain A: R.35, G.38, A.40 Ligand excluded by PLIP CL.54: 3 residues within 4Å: Chain B: R.35, G.38, A.40 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dranow, D.M. et al., Crystal Structure of Lysyl-tRNA synthetase from Stenotrophomonas maltophilia with bound L-lysine. to be published

Release Date

2020-04-08

Peptides

Lysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine--tRNA ligase