SMTL ID : 7c3h.1

Structure of L-lysine oxidase in complex with L-lysine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 38 residues within 4Å: Chain A: V.13, G.14, A.15, G.16, V.17, S.18, F.39, E.40, S.41, G.47, R.48, L.49, I.64, G.65, A.66, M.67, R.68, Y.69, K.250, R.251, V.252, T.285, T.286, C.290, M.294, S.317, Y.369, W.429, N.434, A.438, F.439, G.467, E.468, A.475, W.476, I.477, S.480 Ligands: LYS.2 37 PLIP interactions: 36 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:A.438, A:F.439, A:F.439 Hydrogen bonds: A:G.16, A:V.17, A:S.18, A:S.18, A:S.18, A:S.41, A:S.41, A:R.48, A:A.66, A:M.67, A:R.68, A:R.68, A:V.252, A:V.252, A:E.468, A:I.477, A:S.480, K.2 Water bridges: A:G.19, A:E.40, A:G.47, A:R.48, A:R.48, A:L.49, A:L.49, A:R.251, A:A.287, A:A.287, A:R.293, A:I.478 Salt bridges: A:R.48, A:R.48 pi-Stacking: A:W.476, A:W.476 FAD.6: 39 residues within 4Å: Chain B: V.13, G.14, A.15, G.16, V.17, S.18, F.39, E.40, S.41, G.46, G.47, R.48, L.49, I.64, G.65, A.66, M.67, R.68, Y.69, K.250, R.251, V.252, T.285, T.286, C.290, M.294, S.317, Y.369, W.429, N.434, A.438, F.439, G.467, E.468, A.475, W.476, I.477, S.480 Ligands: LYS.7 37 PLIP interactions: 36 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:A.438, B:F.439 Hydrogen bonds: B:G.16, B:V.17, B:S.18, B:S.18, B:S.18, B:S.41, B:S.41, B:G.46, B:R.48, B:A.66, B:M.67, B:R.68, B:R.68, B:V.252, B:V.252, B:E.468, B:I.477, B:S.480, K.7 Water bridges: B:G.19, B:E.40, B:G.47, B:R.48, B:R.48, B:L.49, B:L.49, B:R.251, B:A.287, B:A.287, B:R.293, B:I.478 Salt bridges: B:R.48, B:R.48 pi-Stacking: B:F.439, B:W.476

2 x LYS: LYSINE(Non-covalent)

LYS.2: 10 residues within 4Å: Chain A: R.68, D.212, F.216, Y.369, W.371, F.439, L.441, A.475, W.476 Ligands: FAD.1 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:F.216, A:F.216, A:W.371, A:F.439, A:A.475, A:W.476 Hydrogen bonds: A:Y.369, A:Y.369, A:A.475 Water bridges: A:E.208, A:E.208 Salt bridges: A:R.68 LYS.7: 10 residues within 4Å: Chain B: R.68, D.212, F.216, Y.369, W.371, F.439, L.441, A.475, W.476 Ligands: FAD.6 12 PLIP interactions: 10 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:F.216, B:F.216, B:W.371, B:F.439, B:A.475, B:W.476 Hydrogen bonds: B:A.475, K.7, K.7 Water bridges: B:E.208, B:E.208 Salt bridges: B:R.68

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: T.197, G.198, R.348, T.349, Y.369, T.370, W.371 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.197, A:T.349 Water bridges: A:R.348, A:R.348, A:W.371 GOL.4: 6 residues within 4Å: Chain A: V.382, D.384, Y.427, C.428, N.431, D.432 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.384, A:C.428, A:C.428 Water bridges: A:D.432 GOL.8: 7 residues within 4Å: Chain B: T.197, G.198, R.348, T.349, Y.369, T.370, W.371 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.197, B:T.349 Water bridges: B:W.371, B:D.374 GOL.9: 6 residues within 4Å: Chain B: V.382, D.384, Y.427, C.428, N.431, D.432 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.384, B:C.428, B:C.428 Water bridges: B:Y.427, B:D.432

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.5: 7 residues within 4Å: Chain A: E.4, L.5, K.496, M.497, W.498, D.499, Y.500 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.498, A:D.499, A:Y.500 Salt bridges: A:E.4, A:E.4, A:D.499 EPE.10: 6 residues within 4Å: Chain B: E.4, L.5, M.497, W.498, D.499, Y.500 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:W.498, B:D.499, B:Y.500 Salt bridges: B:E.4, B:E.4, B:D.499

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kondo, H. et al., Structural basis of strict substrate recognition of l-lysine alpha-oxidase from Trichoderma viride. Protein Sci. (2020)

Release Date

2020-09-23

Peptides

L-lysine oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

L-lysine oxidase