SMTL ID : 6c86.1 (1 other biounit)

Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-Lysylsulfamoyl Adenosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 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.225, A.226, A.247, E.249, R.271, E.273, T.278, H.279, N.280, F.283, E.287, Y.289, E.440, L.441, C.442, N.443, A.444, Y.445, E.447, G.492, W.493, G.494, G.496, R.499, I.510 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.445 Hydrogen bonds: A:E.249, A:R.271, A:R.271, A:E.273, A:E.273, A:N.280, A:E.287, A:E.287, A:Y.289, A:E.440, A:N.443, A:E.447, A:G.496, A:R.499 Salt bridges: A:R.271 pi-Stacking: A:F.283, A:F.283 pi-Cation interactions: A:R.499, A:R.499 KAA.5: 24 residues within 4Å: Chain B: G.225, A.226, A.247, E.249, R.271, E.273, T.278, H.279, N.280, F.283, E.287, Y.289, E.440, L.441, C.442, N.443, Y.445, E.447, G.492, W.493, G.494, G.496, R.499, I.510 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:Y.445 Hydrogen bonds: B:R.271, B:R.271, B:E.273, B:N.280, B:E.287, B:E.440, B:E.440, B:N.443, B:E.447, B:G.496, B:R.499 Water bridges: B:N.269, B:D.498 Salt bridges: B:R.271 pi-Stacking: B:F.283, B:F.283 pi-Cation interactions: B:R.499, B:R.499

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

EDO.2: 5 residues within 4Å: Chain A: W.421, H.422, R.423, E.424, P.426 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.421 EDO.6: 5 residues within 4Å: Chain A: R.203, I.266 Chain B: R.203, E.213 Ligands: EDO.7 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.203, A:R.203, A:I.266, B:R.203, B:E.213 EDO.7: 7 residues within 4Å: Chain A: R.203, E.213, E.215 Chain B: I.199, R.203, I.266 Ligands: EDO.6 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.203, B:R.203, B:I.266, A:R.203 Water bridges: A:E.213, A:E.213 EDO.8: 3 residues within 4Å: Chain B: S.362, Q.363, E.364 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.363, B:E.364

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 1 residues within 4Å: Chain A: T.337 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.337, A:T.337

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

SO4.4: 2 residues within 4Å: Chain A: R.229 Chain B: N.236 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.229 Hydrogen bonds: B:N.236 SO4.9: 5 residues within 4Å: Chain B: H.422, R.423, E.424, K.425, P.426 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.424 Water bridges: B:H.422, B:E.427, B:E.427 SO4.10: 4 residues within 4Å: Chain A: K.35, F.41 Chain B: W.421, Q.453 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.453 Salt bridges: A:K.35

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

CL.11: 1 residues within 4Å: Chain B: C.330 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 Cryptosporidium parvum complexed with L-Lysylsulfamoyl Adenosine. to be published

Release Date

2018-02-28

Peptides

Lysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine--tRNA ligase

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