SMTL ID : 3kve.1

Structure of native L-amino acid oxidase from Vipera ammodytes ammodytes: stabilization of the quaternary structure by divalent ions and structural changes in the dynamic active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

homo-tetramer

Ligands

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

FAD.1: 36 residues within 4Å: Chain A: V.39, G.40, A.41, G.42, M.43, S.44, L.62, E.63, A.64, S.65, G.69, G.70, R.71, V.72, G.87, P.88, M.89, R.90, A.259, R.260, V.261, C.293, T.294, T.295, A.298, Y.372, W.420, Y.425, A.429, I.430, G.456, E.457, G.464, W.465, I.466, T.469 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:Y.372, A:W.420, A:I.430 Hydrogen bonds: A:A.41, A:M.43, A:S.44, A:S.44, A:A.64, A:S.65, A:G.69, A:R.71, A:M.89, A:R.90, A:R.90, A:R.260, A:V.261, A:V.261, A:E.457, A:E.457, A:I.466 Water bridges: A:G.42, A:G.45, A:S.65, A:R.71, A:R.71, A:V.72, A:V.72, A:T.295, A:Y.372, A:D.467, A:T.469 Salt bridges: A:R.71, A:R.71 FAD.4: 37 residues within 4Å: Chain B: V.39, G.40, A.41, G.42, M.43, S.44, L.62, E.63, A.64, S.65, G.69, G.70, R.71, V.72, G.87, P.88, M.89, R.90, A.259, R.260, V.261, C.293, T.294, T.295, A.298, I.302, Y.372, W.420, Y.425, A.429, I.430, G.456, E.457, G.464, W.465, I.466, T.469 34 PLIP interactions: 34 interactions with chain B Hydrophobic interactions: B:Y.372, B:W.420, B:I.430 Hydrogen bonds: B:A.41, B:G.42, B:M.43, B:S.44, B:A.64, B:S.65, B:G.69, B:R.71, B:M.89, B:R.90, B:R.90, B:R.260, B:V.261, B:V.261, B:E.457, B:E.457, B:E.457, B:I.466, B:T.469 Water bridges: B:G.45, B:E.63, B:S.65, B:S.65, B:G.70, B:R.71, B:R.71, B:T.295, B:D.467, B:T.469 Salt bridges: B:R.71, B:R.71 FAD.7: 35 residues within 4Å: Chain C: V.39, G.40, A.41, G.42, M.43, S.44, L.62, E.63, A.64, G.69, G.70, R.71, V.72, G.87, P.88, M.89, R.90, A.259, R.260, V.261, C.293, T.294, T.295, A.298, Y.372, W.420, Y.425, A.429, I.430, G.456, E.457, G.464, W.465, I.466, T.469 30 PLIP interactions: 30 interactions with chain C Hydrophobic interactions: C:W.420, C:I.430 Hydrogen bonds: C:A.41, C:M.43, C:S.44, C:S.44, C:A.64, C:G.69, C:R.71, C:V.72, C:M.89, C:R.90, C:R.90, C:R.260, C:V.261, C:V.261, C:E.457, C:E.457, C:I.466 Water bridges: C:G.42, C:G.45, C:S.65, C:S.65, C:T.295, C:T.295, C:Y.372, C:D.467, C:T.469 Salt bridges: C:R.71, C:R.71 FAD.10: 35 residues within 4Å: Chain D: V.39, G.40, A.41, G.42, M.43, S.44, L.62, E.63, A.64, G.69, G.70, R.71, V.72, G.87, P.88, M.89, R.90, A.259, R.260, V.261, C.293, T.294, T.295, A.298, Y.372, W.420, Y.425, A.429, I.430, G.456, E.457, G.464, W.465, I.466, T.469 34 PLIP interactions: 34 interactions with chain D Hydrophobic interactions: D:W.420, D:I.430 Hydrogen bonds: D:A.41, D:A.41, D:M.43, D:S.44, D:A.64, D:S.65, D:G.69, D:R.71, D:M.89, D:R.90, D:R.90, D:V.261, D:V.261, D:E.457, D:E.457, D:E.457, D:G.464, D:I.466, D:T.469, D:T.469 Water bridges: D:G.42, D:G.45, D:S.65, D:G.70, D:V.72, D:R.90, D:R.260, D:R.260, D:R.260, D:T.469 Salt bridges: D:R.71, D:R.71

4 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 1 residues within 4Å: Chain A: N.172 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.172 NAG.5: 3 residues within 4Å: Chain B: T.171, N.172, Y.175 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.172 NAG.8: 3 residues within 4Å: Chain C: T.171, N.172, Y.175 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.172 NAG.11: 2 residues within 4Å: Chain D: T.171, N.172 2 PLIP interactions: 2 interactions with chain D Water bridges: D:S.174, D:S.174

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 2 residues within 4Å: Chain A: H.75 Chain D: E.279 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: A:H.75, D:E.279, D:E.279, H2O.17, H2O.17 ZN.6: 2 residues within 4Å: Chain B: H.75 Chain C: E.279 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: B:H.75, C:E.279, C:E.279, H2O.12, H2O.12 ZN.9: 2 residues within 4Å: Chain B: E.279 Chain C: H.75 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:E.279, B:E.279, C:H.75, H2O.12 ZN.12: 3 residues within 4Å: Chain A: E.279 Chain D: H.75, M.416 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: D:H.75, A:E.279, A:E.279, H2O.1

Links

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Citation

Gergiova, D. et al., Structure of native L-amino acid oxidase from Vipera ammodytes ammodytes: stabilization of the quaternary structure by divalent ions and structural changes in the dynamic active site. To be Published

Release Date

2010-10-13

Peptides

L-amino acid oxidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-amino acid oxidase