SMTL ID : 1c0p.1

D-AMINO ACIC OXIDASE IN COMPLEX WITH D-ALANINE AND A PARTIALLY OCCUPIED BIATOMIC SPECIES

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 38 residues within 4Å: Chain A: L.12, G.13, S.14, G.15, V.16, I.17, A.36, R.37, D.38, F.48, A.49, S.50, W.52, A.53, G.54, A.55, N.56, R.162, T.163, V.164, A.180, T.181, G.184, I.188, G.201, T.203, Y.225, G.285, R.287, P.288, S.336, S.337, A.338, G.339, Y.340, Q.341 Ligands: DAL.2, PER.3 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:W.52, A:T.203, A:R.287 Hydrogen bonds: A:S.14, A:G.15, A:I.17, A:R.37, A:R.37, A:D.38, A:D.38, A:D.38, A:A.49, A:S.50, A:S.50, A:G.54, A:N.56, A:N.56, A:N.56, A:V.164, A:V.164, A:S.336, A:A.338, A:G.339, A:Y.340, A:Q.341 Water bridges: A:G.18, A:R.37, A:R.37, A:T.58 pi-Cation interactions: A:R.37, A:R.287 FAD.5: 38 residues within 4Å: Chain B: L.12, G.13, S.14, G.15, V.16, I.17, A.36, R.37, D.38, F.48, A.49, S.50, W.52, A.53, G.54, A.55, N.56, R.162, T.163, V.164, A.180, T.181, G.184, I.188, G.201, T.203, Y.225, G.285, R.287, P.288, S.336, S.337, A.338, G.339, Y.340, Q.341 Ligands: DAL.6, PER.7 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:W.52, B:T.203, B:R.287 Hydrogen bonds: B:S.14, B:G.15, B:I.17, B:R.37, B:R.37, B:D.38, B:D.38, B:A.49, B:S.50, B:S.50, B:G.54, B:N.56, B:N.56, B:N.56, B:V.164, B:V.164, B:S.336, B:A.338, B:G.339, B:Y.340, B:Q.341 Water bridges: B:G.18, B:R.37, B:R.37, B:T.58 pi-Cation interactions: B:R.37, B:R.287

2 x DAL: D-ALANINE(Non-covalent)

DAL.2: 8 residues within 4Å: Chain A: F.60, M.215, Y.225, Y.240, R.287, S.337 Ligands: FAD.1, PER.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.225 Hydrogen bonds: A:Y.225, A:S.337 Salt bridges: A:R.287 DAL.6: 8 residues within 4Å: Chain B: F.60, M.215, Y.225, Y.240, R.287, S.337 Ligands: FAD.5, PER.7 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.225 Hydrogen bonds: B:Y.225, B:Y.225, B:Y.240, B:S.337 Salt bridges: B:R.287

2 x PER: PEROXIDE ION(Non-covalent)

PER.3: 4 residues within 4Å: Chain A: R.287, S.337 Ligands: FAD.1, DAL.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.287 PER.7: 4 residues within 4Å: Chain B: R.287, S.337 Ligands: FAD.5, DAL.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.337

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: Q.46 Chain B: R.37, T.47, L.183, G.184, W.245 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.37, B:R.37, B:T.47 GOL.8: 6 residues within 4Å: Chain A: R.37, T.47, L.183, G.184, W.245 Chain B: Q.46 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.37, A:R.37, A:T.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Umhau, S. et al., The x-ray structure of D-amino acid oxidase at very high resolution identifies the chemical mechanism of flavin-dependent substrate dehydrogenation. Proc.Natl.Acad.Sci.USA (2000)

Release Date

2000-11-22

Peptides

D-AMINO ACID OXIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

D-AMINO ACID OXIDASE

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