SMTL ID : 5ts5.1 (1 other biounit)

Crystal structure of L-amino acid oxidase from Bothrops atrox

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 4 residues within 4Å: Chain B: T.171, N.172, S.174 Ligands: NAG.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.172, B:S.174, B:S.174

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

FAD.2: 35 residues within 4Å: Chain A: V.39, G.40, A.41, G.42, M.43, S.44, L.62, E.63, A.64, G.70, R.71, V.72, G.87, P.88, M.89, R.90, L.91, A.259, R.260, V.261, C.293, T.294, T.295, A.298, Y.372, W.420, Y.425, G.429, I.430, G.456, E.457, G.464, W.465, I.466, T.469 37 PLIP interactions: 37 interactions with chain A Hydrophobic interactions: 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:G.70, A:R.71, A:M.89, A:R.90, A:R.90, A:V.261, A:V.261, A:E.457, A:E.457, A:I.466 Water bridges: A:G.45, A:S.65, A:S.65, A:S.65, A:R.71, A:V.72, A:V.72, A:R.260, A:R.260, A:R.260, A:R.260, A:T.295, A:Y.372, A:Y.458, A:D.467, A:T.469 Salt bridges: A:R.71, A:R.71 FAD.8: 34 residues within 4Å: Chain B: V.39, G.40, 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, G.429, I.430, G.456, E.457, G.464, W.465, I.466, T.469 37 PLIP interactions: 37 interactions with chain B Hydrophobic interactions: B:W.420, B:I.430, B:I.430 Hydrogen bonds: B:A.41, B:M.43, B:S.44, B:S.44, B:A.64, B:S.65, B:G.69, B:G.70, 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 Water bridges: B:G.42, B:G.45, B:S.65, B:S.65, B:S.65, B:R.71, B:R.71, B:V.72, B:V.72, B:T.295, B:Y.372, B:D.467, B:T.469 Salt bridges: B:R.71, B:R.71

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: H.314, H.440 Chain B: D.201 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.314, A:H.440, B:D.201, H2O.21 ZN.4: 2 residues within 4Å: Chain A: K.24, E.100 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.100 ZN.7: 3 residues within 4Å: Chain A: D.201 Chain B: H.314, H.440 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.314, B:H.440, A:D.201, H2O.11, H2O.12 ZN.9: 3 residues within 4Å: Chain B: K.334, E.337, N.361 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.337 ZN.10: 1 residues within 4Å: Chain B: E.132 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.132, B:E.132 ZN.11: 3 residues within 4Å: Chain B: N.5, E.8, D.225 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.8, B:D.225, H2O.20, H2O.20

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)

NAG.5: 1 residues within 4Å: Chain A: N.172 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.172 NAG.12: 2 residues within 4Å: Ligands: NAG-FUC.1, NAG-FUC.1 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: F.11, R.12, E.13, Y.16, K.94, H.95 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.11, A:E.13, A:K.94 Water bridges: A:R.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feliciano, P.R. et al., Crystal structure and molecular dynamics studies of L-amino acid oxidase from Bothrops atrox. Toxicon (2017)

Release Date

2017-04-26

Peptides

Amine oxidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Amine oxidase

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