SMTL ID : 6bni.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x LYS: LYSINE(Non-covalent)

LYS.1: 15 residues within 4Å: Chain A: G.225, A.226, A.247, E.249, R.271, E.287, Y.289, N.443, A.444, Y.445, E.447, G.492, W.493, G.494 Ligands: ADN.2 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:Y.445 Hydrogen bonds: A:G.225, A:E.249, A:E.287, A:Y.289, A:N.443, A:E.447 Water bridges: A:R.271, A:R.271 Salt bridges: A:R.271 LYS.13: 15 residues within 4Å: Chain B: G.225, A.226, A.247, E.249, R.271, E.287, Y.289, N.443, A.444, Y.445, E.447, G.492, W.493, G.494 Ligands: ADN.14 11 PLIP interactions: 10 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.445 Hydrogen bonds: B:G.225, B:E.287, B:N.443, B:E.447, K.13 Water bridges: B:R.271, B:R.271, B:R.271, B:R.271 Salt bridges: B:R.271 LYS.23: 15 residues within 4Å: Chain C: G.225, A.226, A.247, E.249, R.271, E.287, Y.289, N.443, A.444, Y.445, E.447, G.492, W.493, G.494 Ligands: ADN.24 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.445 Hydrogen bonds: C:G.225, C:E.249, C:E.287, C:Y.289, C:N.443, C:E.447 Water bridges: C:R.271, C:R.271 Salt bridges: C:R.271 LYS.35: 15 residues within 4Å: Chain D: G.225, A.226, A.247, E.249, R.271, E.287, Y.289, N.443, A.444, Y.445, E.447, G.492, W.493, G.494 Ligands: ADN.36 11 PLIP interactions: 10 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:Y.445 Hydrogen bonds: D:G.225, D:E.287, D:N.443, D:E.447, K.35 Water bridges: D:R.271, D:R.271, D:R.271, D:R.271 Salt bridges: D:R.271

4 x ADN: ADENOSINE(Non-covalent)

ADN.2: 14 residues within 4Å: Chain A: N.269, R.271, E.273, T.278, H.279, N.280, F.283, A.285, E.440, L.441, G.496, R.499, I.510 Ligands: LYS.1 14 PLIP interactions: 12 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:N.269, A:E.273, A:E.273, A:N.280, A:E.440, A:G.496, A:R.499 Water bridges: A:R.271, A:N.443, K.1, K.1 pi-Stacking: A:F.283, A:F.283 pi-Cation interactions: A:R.499 ADN.14: 14 residues within 4Å: Chain B: N.269, R.271, E.273, T.278, H.279, N.280, F.283, A.285, E.440, L.441, G.496, R.499, I.510 Ligands: LYS.13 15 PLIP interactions: 13 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:N.269, B:R.271, B:E.273, B:N.280, B:E.440, B:G.496, B:R.499 Water bridges: B:N.443, B:G.494, B:D.498, K.13, K.13 pi-Stacking: B:F.283, B:F.283 pi-Cation interactions: B:R.499 ADN.24: 14 residues within 4Å: Chain C: N.269, R.271, E.273, T.278, H.279, N.280, F.283, A.285, E.440, L.441, G.496, R.499, I.510 Ligands: LYS.23 14 PLIP interactions: 2 Ligand-Ligand interactions, 12 interactions with chain C Water bridges: K.23, K.23, C:R.271, C:N.443 Hydrogen bonds: C:N.269, C:E.273, C:E.273, C:N.280, C:E.440, C:G.496, C:R.499 pi-Stacking: C:F.283, C:F.283 pi-Cation interactions: C:R.499 ADN.36: 14 residues within 4Å: Chain D: N.269, R.271, E.273, T.278, H.279, N.280, F.283, A.285, E.440, L.441, G.496, R.499, I.510 Ligands: LYS.35 15 PLIP interactions: 13 interactions with chain D, 2 Ligand-Ligand interactions Hydrogen bonds: D:N.269, D:R.271, D:E.273, D:N.280, D:E.440, D:G.496, D:R.499 Water bridges: D:N.443, D:G.494, D:D.498, K.35, K.35 pi-Stacking: D:F.283, D:F.283 pi-Cation interactions: D:R.499

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

SO4.3: 5 residues within 4Å: Chain A: R.229 Chain B: N.236 Chain C: R.229 Chain D: N.236 Ligands: SO4.25 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 interactions with chain D, 1 interactions with chain C Salt bridges: A:R.229, C:R.229 Hydrogen bonds: B:N.236, D:N.236 Water bridges: B:N.236 SO4.4: 4 residues within 4Å: Chain A: E.273, G.274, D.276, H.279 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.274, A:G.274 Salt bridges: A:H.279 SO4.15: 4 residues within 4Å: Chain A: K.35, F.41 Chain B: W.421, Q.453 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.35 Hydrogen bonds: B:W.421 Water bridges: B:Q.453 SO4.16: 4 residues within 4Å: Chain B: E.273, G.274, D.276, H.279 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.274, B:G.274 Salt bridges: B:H.279 SO4.17: 6 residues within 4Å: Chain B: W.421, H.422, R.423, E.424, K.425, P.426 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.422 Water bridges: B:E.427, B:E.427 SO4.18: 4 residues within 4Å: Chain B: K.58, Y.59, V.62, Y.66 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.58 SO4.25: 5 residues within 4Å: Chain A: R.229 Chain B: N.236 Chain C: R.229 Chain D: N.236 Ligands: SO4.3 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 interactions with chain D, 1 interactions with chain C Salt bridges: A:R.229, C:R.229 Hydrogen bonds: B:N.236, D:N.236 Water bridges: D:N.236 SO4.26: 4 residues within 4Å: Chain C: E.273, G.274, D.276, H.279 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.274, C:G.274 Salt bridges: C:H.279 SO4.37: 4 residues within 4Å: Chain C: K.35, F.41 Chain D: W.421, Q.453 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Salt bridges: C:K.35 Hydrogen bonds: D:W.421 Water bridges: D:Q.453 SO4.38: 4 residues within 4Å: Chain D: E.273, G.274, D.276, H.279 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.274, D:G.274 Salt bridges: D:H.279 SO4.39: 6 residues within 4Å: Chain D: W.421, H.422, R.423, E.424, K.425, P.426 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.422 Water bridges: D:E.427, D:E.427 SO4.40: 4 residues within 4Å: Chain D: K.58, Y.59, V.62, Y.66 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.58

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

EDO.5: 4 residues within 4Å: Chain A: G.65, I.67, K.140, F.147 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: I.199, R.203, I.266 Chain B: R.203, E.213, E.215 Ligands: EDO.19 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: M.218, I.266, G.267, K.268 Chain B: M.218, I.266, G.267, K.268 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: L.250, Y.251, Q.254, D.476, T.478 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: M.415, P.417, R.431, N.443 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: E.399, T.400, C.402, T.403, L.437, G.438 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: W.421, H.422, R.423, E.424, K.425, P.426 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: R.203, E.213, E.215 Chain B: R.203, I.266 Ligands: EDO.6 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: T.400, T.403, L.437, G.438 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain B: I.222, L.250, Y.251, Q.254, D.476, T.478, F.479 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: I.222, Y.223, G.224, R.245, I.246, A.247 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain C: G.65, I.67, K.140, F.147 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain C: I.199, R.203, I.266 Chain D: R.203, E.213, E.215 Ligands: EDO.41 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain C: M.218, I.266, G.267, K.268 Chain D: M.218, I.266, G.267, K.268 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain C: L.250, Y.251, Q.254, D.476, T.478 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain C: M.415, P.417, R.431, N.443 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain C: E.399, T.400, C.402, T.403, L.437, G.438 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain C: W.421, H.422, R.423, E.424, K.425, P.426 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain C: R.203, E.213, E.215 Chain D: R.203, I.266 Ligands: EDO.28 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain D: T.400, T.403, L.437, G.438 Ligand excluded by PLIP EDO.43: 7 residues within 4Å: Chain D: I.222, L.250, Y.251, Q.254, D.476, T.478, F.479 Ligand excluded by PLIP EDO.44: 6 residues within 4Å: Chain D: I.222, Y.223, G.224, R.245, I.246, A.247 Ligand excluded by PLIP

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

NA.12: 1 residues within 4Å: Chain A: T.337 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.337, A:T.337 Water bridges: A:T.337, A:T.337 NA.34: 1 residues within 4Å: Chain C: T.337 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.337 Water bridges: C:T.337, C:T.337, C:T.337, C:T.337, C:T.337

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-lysine and Adenosine. to be published

Release Date

2018-02-14

Peptides

Lysine--tRNA ligase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Lysine--tRNA ligase

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