SMTL ID : 7eij.1

Ancestral L-Lys oxidase K387A variant (L-Arg binding form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 35 residues within 4Å: Chain A: I.23, G.24, G.26, T.27, S.28, F.50, D.51, M.52, G.57, G.58, R.59, L.60, G.75, G.76, M.77, R.78, Y.288, N.311, K.312, L.313, A.351, M.352, P.353, S.356, L.360, W.509, P.513, F.514, G.517, G.547, E.548, G.555, W.556, V.557, A.560 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:W.509 Hydrogen bonds: A:G.26, A:T.27, A:S.28, A:M.52, A:R.59, A:L.60, A:G.76, A:M.77, A:R.78, A:R.78, A:L.313, A:L.313, A:E.548, A:V.557 Water bridges: A:G.29, A:N.53, A:A.549, A:E.558 Salt bridges: A:R.59, A:R.59 FAD.2: 38 residues within 4Å: Chain B: I.23, G.24, G.26, T.27, S.28, F.50, D.51, M.52, G.57, G.58, R.59, L.60, G.75, G.76, M.77, R.78, Y.288, N.311, K.312, L.313, A.351, M.352, P.353, S.356, L.360, Y.436, W.509, P.513, F.514, G.517, Y.518, G.547, E.548, G.555, W.556, V.557, A.560 Ligands: ARG.3 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:Y.436, B:W.509, B:Y.518, B:Y.518 Hydrogen bonds: B:T.27, B:T.27, B:S.28, B:M.52, B:N.53, B:R.59, B:G.76, B:M.77, B:R.78, B:R.78, B:Y.288, B:L.313, B:L.313, B:E.548, B:V.557 Water bridges: B:G.26, B:G.26, B:G.58, B:E.548, B:E.558 Salt bridges: B:R.59, B:R.59

1 x ARG: ARGININE(Non-covalent)

ARG.3: 10 residues within 4Å: Chain B: Y.255, N.258, Y.270, E.385, Y.518, H.519, Q.554, G.555, W.556 Ligands: FAD.2 11 PLIP interactions: 9 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.518 Hydrogen bonds: B:N.258, B:H.519, B:H.519, B:H.519, B:G.555, R.3, R.3 Salt bridges: B:R.78, B:E.385 pi-Cation interactions: B:W.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sugiura, S. et al., Catalytic mechanism of ancestral L-lysine oxidase assigned by sequence data mining. J.Biol.Chem. (2021)

Release Date

2021-08-11

Peptides

FAD dependent L-Lys oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

FAD dependent L-Lys oxidase

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