SMTL ID : 4r34.2 (1 other biounit)

X-ray structure of the tryptophan lyase NosL with Tryptophan, 5'-deoxyadenosine and methionine bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x MET: METHIONINE(Non-covalent)

MET.1: 12 residues within 4Å: Chain A: Y.110, T.161, G.162, E.163, N.195, G.197, K.244, R.250, Q.383 Ligands: 5AD.2, SAH.3, SF4.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.161 Water bridges: A:G.197, A:F.222 Salt bridges: A:K.244, A:R.250 MET.15: 12 residues within 4Å: Chain B: Y.110, T.161, G.162, E.163, N.195, G.197, K.244, R.250, Q.383 Ligands: 5AD.16, SAH.17, SF4.18 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.161, B:N.195 Water bridges: B:G.197, B:F.222 Salt bridges: B:K.244, B:R.250

2 x 5AD: 5'-DEOXYADENOSINE(Non-covalent)

5AD.2: 16 residues within 4Å: Chain A: Y.110, M.121, L.160, F.222, E.224, L.270, R.304, M.305, R.306, A.308, R.343, Q.383, F.384 Ligands: MET.1, SAH.3, TRP.5 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.160 Hydrogen bonds: A:E.224, A:R.306, A:R.306, A:R.343, A:Q.383, W.5 Water bridges: A:N.195 pi-Stacking: A:F.384 5AD.16: 16 residues within 4Å: Chain B: Y.110, M.121, L.160, F.222, E.224, L.270, R.304, M.305, R.306, A.308, R.343, Q.383, F.384 Ligands: MET.15, SAH.17, TRP.19 9 PLIP interactions: 8 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:L.160 Hydrogen bonds: B:E.224, B:R.306, B:R.306, B:R.343, B:Q.383, W.19 Water bridges: B:N.195 pi-Stacking: B:F.384

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

SAH.3: 25 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: MET.1, 5AD.2, SF4.4, TRP.5 12 PLIP interactions: 10 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:G.162, A:G.197, A:R.306, A:R.306, A:R.343, A:Q.383, W.5 Water bridges: A:N.195 Salt bridges: A:K.244, A:R.250 pi-Stacking: A:F.384 Hydrophobic interactions: M.1 SAH.17: 25 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: MET.15, 5AD.16, SF4.18, TRP.19 12 PLIP interactions: 11 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:G.162, B:N.195, B:G.197, B:R.306, B:R.306, B:R.343, B:Q.383, W.19 Water bridges: B:N.195 Salt bridges: B:K.244, B:R.250 pi-Stacking: B:F.384

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

SF4.4: 11 residues within 4Å: Chain A: C.115, S.117, C.119, C.122, M.124, R.125, E.163, K.244, Q.383 Ligands: MET.1, SAH.3 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Ligand interactions Salt bridges: A:E.224 Metal complexes: A:C.115, A:C.119, A:C.122, MET.1, SAH.3 SF4.18: 11 residues within 4Å: Chain B: C.115, S.117, C.119, C.122, M.124, R.125, E.163, K.244, Q.383 Ligands: MET.15, SAH.17 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.17

2 x TRP: TRYPTOPHAN(Non-covalent)

TRP.5: 15 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: 5AD.2, SAH.3 15 PLIP interactions: 15 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 pi-Cation interactions: A:R.343 TRP.19: 15 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: 5AD.16, SAH.17 14 PLIP interactions: 14 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 pi-Cation interactions: B:R.343

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: H.104, R.191, Y.193, T.218, D.299, R.337 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.218, A:T.218 Water bridges: A:D.299, A:D.299, A:R.337, A:R.337 GOL.7: 4 residues within 4Å: Chain A: H.150, H.151, R.393, P.412 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.393, A:P.412 Water bridges: A:H.151, A:R.393, A:R.393 GOL.8: 7 residues within 4Å: Chain A: T.230, R.233, F.234, L.273, H.274, D.275, R.312 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.230, A:R.233, A:D.275, A:D.275, A:R.312, A:R.312 GOL.20: 6 residues within 4Å: Chain B: H.104, R.191, Y.193, T.218, 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:R.337, B:R.337 GOL.21: 4 residues within 4Å: Chain B: H.150, H.151, R.393, P.412 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.151, B:R.393, B:P.412 Water bridges: B:R.393, B:R.393 GOL.22: 7 residues within 4Å: Chain B: T.230, R.233, F.234, L.273, H.274, D.275, R.312 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.233, B:H.274, B:D.275, B:D.275, B:R.312, B:R.312 Water bridges: B:T.230, B:T.230

8 x BR: BROMIDE ION(Non-covalent)

BR.9: 2 residues within 4Å: Chain A: R.100, R.102 Ligand excluded by PLIP BR.10: 2 residues within 4Å: Chain A: R.155, H.408 Ligand excluded by PLIP BR.11: 3 residues within 4Å: Chain A: H.150, L.187 Ligands: ZN.13 Ligand excluded by PLIP BR.14: 4 residues within 4Å: Chain A: M.305, R.306, P.307, K.310 Ligand excluded by PLIP BR.23: 2 residues within 4Å: Chain B: R.100, R.102 Ligand excluded by PLIP BR.24: 2 residues within 4Å: Chain B: R.155, H.408 Ligand excluded by PLIP BR.25: 3 residues within 4Å: Chain B: H.150, L.187 Ligands: ZN.27 Ligand excluded by PLIP BR.28: 4 residues within 4Å: Chain B: M.305, R.306, P.307, K.310 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.12: 3 residues within 4Å: Chain A: E.400, V.406, F.409 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.406, A:F.409 Water bridges: A:F.409 NA.26: 3 residues within 4Å: Chain B: E.400, V.406, F.409 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.400, B:V.406 Water bridges: B:D.407

2 x ZN: ZINC ION(Non-covalent)

ZN.13: 3 residues within 4Å: Chain A: E.146, H.150 Ligands: BR.11 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.146, A:H.150, H2O.13 ZN.27: 3 residues within 4Å: Chain B: E.146, H.150 Ligands: BR.25 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.146, B:H.150, H2O.29

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
B

B
B

NosL

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