SMTL ID : 2y4g.1

Structure of the Tirandamycin-bound FAD-dependent tirandamycin oxidase TamL in P212121 space group

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-dimer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 32 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.3 27 PLIP interactions: 27 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:C.152, 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 Water bridges: A:R.88, A:G.91 FAD.12: 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, 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.14 26 PLIP interactions: 26 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:C.152, 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 Water bridges: B:R.88, B:G.91

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

MG.2: 3 residues within 4Å: Chain A: D.154 Chain B: R.353 Ligands: CL.7 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: D.360 Ligands: TIR.3 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain A: R.353 Chain B: D.154 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Ligands: TIR.14 No protein-ligand interaction detected (PLIP)

2 x TIR: TIRANDAMYCIN E(Non-covalent)

TIR.3: 14 residues within 4Å: Chain A: Y.94, C.152, Y.294, D.362, M.363, T.364, A.367, I.369, A.403, V.433, T.435, Y.477 Ligands: FAD.1, MG.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.369, A:A.403, A:V.433, A:T.435, A:Y.477 Hydrogen bonds: A:Y.477 Water bridges: A:T.435 TIR.14: 16 residues within 4Å: Chain B: Y.94, C.152, Y.294, G.359, D.362, M.363, G.365, A.367, I.369, A.403, V.431, V.433, T.435, Y.477 Ligands: FAD.12, MG.15 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.367, B:I.369, B:A.403, B:V.431, B:V.433, B:Y.477 Hydrogen bonds: B:G.365, B:T.435, B:Y.477

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

CL.5: 4 residues within 4Å: Chain A: S.67, A.68, V.226, R.227 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: C.152, P.153, D.154 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: E.51, H.92, D.154, M.363 Ligands: MG.2 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: W.494, S.524, R.526 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: K.410, V.414 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 7 residues within 4Å: Chain A: R.54, E.95, K.368, V.446, R.450, V.480, D.481 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.54, A:E.95, A:K.368, A:R.450, A:D.481 Water bridges: A:R.54 GOL.10: 6 residues within 4Å: Chain A: A.78, V.79, G.82, K.83, R.84, R.520 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.78, A:G.82, A:R.520, A:R.520 Water bridges: A:G.82, A:K.83, A:V.85 GOL.11: 9 residues within 4Å: Chain A: L.482, A.483, D.484, E.485, N.488, G.491, V.492, P.493, W.494 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.483, A:N.488, A:N.488, A:G.491, A:W.494 GOL.17: 5 residues within 4Å: Chain B: V.79, G.82, K.83, R.84, R.520 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.82, B:V.85, B:R.520, B:R.520 Water bridges: B:R.84

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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