SMTL ID : 2y3r.1 (1 other biounit)

Structure of the tirandamycin-bound FAD-dependent tirandamycin oxidase TamL in P21 space group

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 33 residues within 4Å: Chain A: V.87, R.88, S.89, G.90, G.91, H.92, C.93, Y.94, F.97, V.98, A.128, G.150, A.151, C.152, V.155, G.156, G.158, G.159, H.160, L.162, G.165, Y.166, G.219, G.220, G.223, V.224, V.225, M.363, Y.474, N.476, Y.477 Ligands: TIR.2, GOL.4 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:H.92, A:Y.94, A:V.155 Hydrogen bonds: A:V.87, A:V.87, A:S.89, A:S.89, A:G.90, A:G.91, A:H.92, A:C.93, A:A.151, A:G.156, A:G.156, A:G.159, A:H.160, A:Y.166, A:Y.166, A:G.220, A:V.225, A:V.225, A:N.476, A:N.476, A:Y.477, A:H.521 Water bridges: A:R.88, A:G.91, A:G.219 FAD.6: 32 residues within 4Å: Chain B: V.87, R.88, S.89, G.90, G.91, H.92, C.93, Y.94, F.97, V.98, A.128, G.150, A.151, C.152, V.155, G.156, G.158, G.159, H.160, G.165, Y.166, G.219, G.220, G.223, V.224, V.225, M.363, Y.474, N.476, Y.477 Ligands: TRK.7, GOL.9 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:H.92, B:Y.94, B:V.155 Hydrogen bonds: B:V.87, B:S.89, B:S.89, B:G.90, B:G.91, B:H.92, B:C.93, B:A.151, B:G.156, B:G.156, B:G.159, B:H.160, B:Y.166, B:Y.166, B:G.220, B:V.225, B:V.225, B:N.476, B:N.476, B:Y.477

1 x TIR: TIRANDAMYCIN E(Non-covalent)

TIR.2: 17 residues within 4Å: Chain A: Y.94, C.152, Y.294, G.359, D.362, M.363, T.364, A.367, I.369, A.403, V.431, V.433, T.435, Y.477 Ligands: FAD.1, MG.3, GOL.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.369, A:A.403, A:V.431, A:V.433, A:T.435, A:Y.477 Hydrogen bonds: A:Y.477 Water bridges: A:D.360, A:D.360, A:T.435

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 2 residues within 4Å: Chain A: D.360 Ligands: TIR.2 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: TRK.7 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: Y.94, C.152, G.359, D.360, G.361 Ligands: FAD.1, TIR.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.94, A:D.360, A:D.360, A:D.360, A:G.361 Water bridges: A:D.362, A:D.362 GOL.9: 6 residues within 4Å: Chain B: Y.94, G.359, D.360, G.361 Ligands: FAD.6, TRK.7 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.94, B:D.360, B:D.360, B:D.360, B:G.361 Water bridges: B:D.362 GOL.10: 8 residues within 4Å: Chain B: R.54, F.55, E.95, K.368, V.446, R.450, V.480, D.481 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.54, B:R.54, B:K.368, B:R.450, B:R.450

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: D.96, F.97, N.100, H.521, A.522 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: D.96, F.97, N.100, H.521, A.522 Ligand excluded by PLIP

1 x TRK: TIRANDAMYCIN D(Non-covalent)

TRK.7: 17 residues within 4Å: Chain B: Y.94, C.152, Y.294, G.359, D.362, M.363, T.364, A.367, I.369, A.403, V.431, V.433, T.435, Y.477 Ligands: FAD.6, MG.8, GOL.9 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.369, B:A.403, B:V.431, B:V.433, B:T.435, B:Y.477 Hydrogen bonds: B:Y.477 Water bridges: B:T.435

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carlson, J.C. et al., Tirandamycin Biosynthesis is Mediated by Co-Dependent Oxidative Enzymes. Nat.Chem (2011)

Release Date

2011-06-29

Peptides

TAML: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

TAML

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