SMTL ID : 4ycu.1

Crystal structure of cladosporin in complex with human lysyl-tRNA synthetase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-4-2-mer

Ligands

4 x KRS: cladosporin(Non-covalent)

KRS.1: 17 residues within 4Å: Chain A: R.255, E.257, T.262, H.263, N.264, F.267, T.269, E.426, I.427, C.428, N.429, G.480, M.481, G.482, R.485, I.496 Ligands: LYS.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:H.263, A:T.269, A:N.429 Hydrogen bonds: A:E.257, A:N.264 Water bridges: A:E.257 Salt bridges: A:R.485 pi-Stacking: A:H.263, A:F.267 KRS.5: 17 residues within 4Å: Chain B: R.255, E.257, T.262, H.263, N.264, F.267, T.269, E.426, I.427, C.428, N.429, G.480, M.481, G.482, R.485, I.496 Ligands: LYS.6 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:H.263, B:T.269, B:E.426, B:N.429 Hydrogen bonds: B:E.257, B:N.264 Water bridges: B:E.257, B:D.484 Salt bridges: B:R.485 pi-Stacking: B:H.263, B:F.267 KRS.9: 17 residues within 4Å: Chain D: R.255, E.257, T.262, H.263, N.264, F.267, T.269, E.426, I.427, C.428, N.429, G.480, M.481, G.482, R.485, I.496 Ligands: LYS.10 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:H.263, D:T.269, D:N.429 Hydrogen bonds: D:E.257, D:E.257, D:N.264 Water bridges: D:E.257, D:D.484 Salt bridges: D:R.485 pi-Stacking: D:H.263, D:F.267 KRS.13: 17 residues within 4Å: Chain E: R.255, E.257, T.262, H.263, N.264, F.267, T.269, E.426, I.427, C.428, N.429, G.480, M.481, G.482, R.485, I.496 Ligands: LYS.14 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:H.263, E:T.269, E:E.426, E:N.429 Hydrogen bonds: E:E.257, E:E.257, E:N.264 Water bridges: E:E.257 Salt bridges: E:R.485 pi-Stacking: E:H.263, E:F.267

4 x LYS: LYSINE(Non-covalent)

LYS.2: 15 residues within 4Å: Chain A: G.209, A.210, A.231, E.233, R.255, E.271, Y.273, N.429, A.430, Y.431, E.433, G.478, W.479, G.480 Ligands: KRS.1 13 PLIP interactions: 12 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:Y.431 Hydrogen bonds: A:G.209, A:E.233, A:E.271, A:E.271, A:Y.273, A:N.429, A:E.433, K.2 Water bridges: A:R.255, A:R.255, A:R.255 Salt bridges: A:R.255 LYS.6: 15 residues within 4Å: Chain B: G.209, A.210, A.231, E.233, R.255, E.271, Y.273, N.429, A.430, Y.431, E.433, G.478, W.479, G.480 Ligands: KRS.5 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:Y.431 Hydrogen bonds: B:G.209, B:E.271, B:N.429, B:E.433 Water bridges: B:R.255, B:R.255, B:R.255 Salt bridges: B:R.255 LYS.10: 15 residues within 4Å: Chain D: G.209, A.210, A.231, E.233, R.255, E.271, Y.273, N.429, A.430, Y.431, E.433, G.478, W.479, G.480 Ligands: KRS.9 11 PLIP interactions: 10 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:Y.431 Hydrogen bonds: D:G.209, D:E.271, D:N.429, D:E.433, K.10 Water bridges: D:R.255, D:R.255, D:R.255, D:Y.431 Salt bridges: D:R.255 LYS.14: 15 residues within 4Å: Chain E: G.209, A.210, A.231, E.233, R.255, E.271, Y.273, N.429, A.430, Y.431, E.433, G.478, W.479, G.480 Ligands: KRS.13 11 PLIP interactions: 11 interactions with chain E, Hydrophobic interactions: E:Y.431 Hydrogen bonds: E:G.209, E:E.233, E:Y.273, E:N.429, E:E.433 Water bridges: E:R.255, E:R.255, E:R.255, E:Y.431 Salt bridges: E:R.255

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: R.63, H.65, R.80, G.81, E.82, G.83, I.167, R.173 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.63, A:G.81, A:G.83, A:R.173 GOL.4: 3 residues within 4Å: Chain A: D.377, E.385, E.419 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.385, A:E.419 GOL.7: 6 residues within 4Å: Chain B: Y.279, M.283, R.325, N.327, C.395, D.396 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.327, B:D.396 Water bridges: B:K.411 GOL.8: 5 residues within 4Å: Chain B: D.377, E.385, E.419, F.421, E.426 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.385, B:E.426 Water bridges: B:E.385 GOL.11: 8 residues within 4Å: Chain D: R.63, H.65, R.80, G.81, E.82, G.83, I.167, R.173 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.63, D:G.81, D:G.83, D:R.173 GOL.12: 3 residues within 4Å: Chain D: D.377, E.385, E.419 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.385, D:E.419 Water bridges: D:D.377, D:E.385, D:E.385 GOL.15: 6 residues within 4Å: Chain E: Y.279, M.283, R.325, N.327, C.395, D.396 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Y.279, E:N.327, E:D.396 Water bridges: E:K.411 GOL.16: 5 residues within 4Å: Chain E: D.377, E.385, E.419, F.421, E.426 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.385, E:E.426 Water bridges: E:E.419

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fang, P. et al., Structural Basis for Specific Inhibition of tRNA Synthetase by an ATP Competitive Inhibitor. Chem. Biol. (2015)

Release Date

2015-06-10

Peptides

Lysine--tRNA ligase: ABDE
Aminoacyl tRNA synthase complex-interacting multifunctional protein 2: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
A

E
B

C
C

F
C

Lysine--tRNA ligase

Aminoacyl tRNA synthase complex-interacting multifunctional protein 2

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