SMTL ID : 4r33.1 (1 other biounit)

X-ray structure of the tryptophan lyase NosL with Tryptophan and S-adenosyl-L-homocysteine bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 23 residues within 4Å: Chain A: Y.110, M.121, C.122, L.160, T.161, G.162, E.163, N.195, G.197, F.222, E.224, K.244, R.250, L.270, R.304, M.305, R.306, A.308, R.343, Q.383, F.384 Ligands: SF4.2, TRP.3 13 PLIP interactions: 12 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:N.195, A:G.197, A:E.224, A:R.306, A:R.306, A:R.343, A:Q.383, W.3 Water bridges: A:N.195, A:N.195 Salt bridges: A:K.244, A:R.250 pi-Stacking: A:F.384 SAH.6: 23 residues within 4Å: Chain B: Y.110, M.121, C.122, L.160, T.161, G.162, E.163, N.195, G.197, F.222, E.224, K.244, R.250, L.270, R.304, M.305, R.306, A.308, R.343, Q.383, F.384 Ligands: SF4.7, TRP.8 13 PLIP interactions: 12 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:N.195, B:G.197, B:E.224, B:R.306, B:R.306, B:R.343, B:Q.383, W.8 Water bridges: B:N.195, B:N.195 Salt bridges: B:K.244, B:R.250 pi-Stacking: B:F.384

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.2: 8 residues within 4Å: Chain A: C.115, S.117, C.119, C.122, M.124, R.125, K.244 Ligands: SAH.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Salt bridges: A:E.224 Metal complexes: A:C.115, A:C.119, A:C.122, SAH.1 SF4.7: 8 residues within 4Å: Chain B: C.115, S.117, C.119, C.122, M.124, R.125, K.244 Ligands: SAH.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Salt bridges: B:E.224 Metal complexes: B:C.115, B:C.119, B:C.122, SAH.6

2 x TRP: TRYPTOPHAN(Non-covalent)

TRP.3: 14 residues within 4Å: Chain A: F.106, P.108, Y.110, L.160, F.222, T.341, T.342, R.343, S.360, G.362, P.364, F.384, V.386 Ligands: SAH.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:P.108, A:P.108, A:L.160, A:P.364, A:F.384, A:V.386 Hydrogen bonds: A:Y.110, A:Y.110, A:R.343, A:R.343, A:S.360 Water bridges: A:N.195, A:S.301 Salt bridges: A:R.343 TRP.8: 14 residues within 4Å: Chain B: F.106, P.108, Y.110, L.160, F.222, T.341, T.342, R.343, S.360, G.362, P.364, F.384, V.386 Ligands: SAH.6 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:P.108, B:P.108, B:L.160, B:P.364, B:F.384, B:V.386 Hydrogen bonds: B:Y.110, B:R.343, B:R.343, B:S.360 Water bridges: B:N.195, B:S.301 Salt bridges: B:R.343

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: H.104, R.191, Y.193, T.218, Y.264, D.299, R.337 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.218, A:T.218 Water bridges: A:D.299, A:R.337 GOL.9: 7 residues within 4Å: Chain B: H.104, R.191, Y.193, T.218, Y.264, D.299, R.337 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.193, B:T.218 Water bridges: B:D.299, B:D.299, B:R.337

2 x K: POTASSIUM ION(Non-covalent)

K.5: 3 residues within 4Å: Chain A: E.400, V.406, F.409 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.400, A:V.406, A:F.409, H2O.2 K.10: 3 residues within 4Å: Chain B: E.400, V.406, F.409 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.400, B:V.406, B:F.409, H2O.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nicolet, Y. et al., Crystal Structure of Tryptophan Lyase (NosL): Evidence for Radical Formation at the Amino Group of Tryptophan. Angew.Chem.Int.Ed.Engl. (2014)

Release Date

2014-09-17

Peptides

NosL: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

NosL

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