SMTL ID : 5yb6.2 (1 other biounit)

L-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 - L-lysine complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 41 residues within 4Å: Chain A: V.71, G.72, G.74, I.75, A.76, Y.94, E.95, A.96, S.97, K.98, G.100, G.101, R.102, L.103, L.118, G.119, G.120, M.121, R.122, F.123, P.124, G.320, V.321, T.350, C.351, L.355, I.360, S.383, Y.436, W.483, H.488, F.489, A.492, F.493, G.527, D.528, A.535, W.536, V.537, A.540 Ligands: LYS.3 33 PLIP interactions: 32 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:A.492 Hydrogen bonds: A:G.72, A:G.74, A:A.76, A:A.96, A:S.97, A:R.102, A:G.120, A:M.121, A:R.122, A:R.122, A:V.321, A:V.321, A:H.488, A:D.528, A:D.528, A:D.528, A:V.537, K.3 Water bridges: A:G.77, A:E.95, A:K.98, A:R.102, A:R.102, A:L.103, A:L.103, A:S.127, A:Q.352, A:Y.436, A:Y.436 Salt bridges: A:R.102, A:R.102 pi-Stacking: A:F.493 FAD.5: 40 residues within 4Å: Chain B: V.71, G.72, A.73, G.74, I.75, A.76, Y.94, E.95, A.96, K.98, G.100, G.101, R.102, L.103, L.118, G.119, G.120, M.121, R.122, F.123, G.320, V.321, T.350, C.351, L.355, I.360, S.383, Y.436, W.483, H.488, F.489, A.492, F.493, G.527, D.528, A.535, W.536, V.537, A.540 Ligands: LYS.7 28 PLIP interactions: 27 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:A.492, B:F.493 Hydrogen bonds: B:A.73, B:I.75, B:A.76, B:A.96, B:R.102, B:G.120, B:M.121, B:R.122, B:R.122, B:V.321, B:V.321, B:D.528, B:D.528, B:V.537, K.7 Water bridges: B:G.74, B:K.98, B:G.101, B:R.102, B:R.102, B:L.103, B:L.103, B:E.538 Salt bridges: B:R.102, B:R.102 pi-Stacking: B:F.493

2 x PG6: 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE(Non-covalent)

PG6.2: 10 residues within 4Å: Chain A: L.159, E.160, Q.162, Y.164, P.173, L.175, Q.240, V.244 Chain B: K.370, D.580 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.162, A:Y.164, A:Q.240 Water bridges: B:K.370 PG6.6: 8 residues within 4Å: Chain A: K.370, D.580 Chain B: L.159, E.160, Q.162, Y.164, F.176, Q.240 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.162, B:Q.240, A:K.370 Water bridges: B:E.160

4 x LYS: LYSINE(Non-covalent)

LYS.3: 10 residues within 4Å: Chain A: R.122, W.255, D.258, M.381, Y.436, W.438, F.493, A.535, W.536 Ligands: FAD.1 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:W.255, A:W.255, A:W.438, A:A.535 Hydrogen bonds: A:D.258, A:Y.436, A:Y.436, A:A.535 Water bridges: A:N.261, A:N.261, A:Q.278 Salt bridges: A:R.122 LYS.4: 10 residues within 4Å: Chain A: T.357, E.364, Q.369, W.372, D.376 Chain B: E.160, G.161, D.413, R.414, L.415 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A, Hydrogen bonds: B:E.160, B:G.161, B:D.413, B:L.415, A:T.357 Water bridges: B:R.414, B:K.444, B:K.444, B:K.444 Salt bridges: B:K.444 Hydrophobic interactions: A:W.372, A:W.372 LYS.7: 10 residues within 4Å: Chain B: R.122, W.255, D.258, M.381, Y.436, W.438, F.493, A.535, W.536 Ligands: FAD.5 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:W.255, B:W.438, B:F.493, B:A.535 Hydrogen bonds: B:Y.436, B:A.535 Water bridges: B:D.258, B:D.258, B:N.261, B:E.265, B:Q.278, B:P.534 Salt bridges: B:R.122 LYS.8: 10 residues within 4Å: Chain A: E.160, G.161, D.413, R.414, L.415 Chain B: T.357, E.364, Q.369, W.372, D.376 14 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: A:G.161, A:D.413, A:L.415, B:T.357, B:T.357, B:D.376, K.8 Water bridges: A:E.160, A:K.444, A:K.444, A:K.444 Salt bridges: A:K.444 Hydrophobic interactions: B:W.372, B:W.372

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Im, D. et al., Ligand complex structures of l-amino acid oxidase/monooxygenase from. FEBS Open Bio (2018)

Release Date

2018-02-07

Peptides

L-amino acid oxidase/monooxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

L-amino acid oxidase/monooxygenase

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