SMTL ID : 5lmz.1

Fluorinase from Streptomyces sp. MA37

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-hexamer

Ligands

6 x 1DA: 1-DEAZA-ADENOSINE(Non-covalent)

1DA.1: 20 residues within 4Å: Chain A: F.216, N.218, F.257, A.279, R.280, N.281, A.282, A.283 Chain C: D.19, L.20, W.53, T.79, Y.80, P.81, T.83, T.158, F.159, Y.160, S.161, R.162 15 PLIP interactions: 9 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:D.19, C:D.19, C:W.53, C:T.79, C:Y.80, C:F.159, C:S.161, A:N.218, A:N.218 pi-Stacking: C:W.53, C:W.53, A:F.257, A:F.257 Hydrophobic interactions: A:F.257 Water bridges: A:R.280 1DA.4: 20 residues within 4Å: Chain B: F.216, N.218, F.257, A.279, R.280, N.281, A.282, A.283 Chain F: D.19, L.20, W.53, T.79, Y.80, P.81, T.83, T.158, F.159, Y.160, S.161, R.162 12 PLIP interactions: 6 interactions with chain F, 6 interactions with chain B Hydrogen bonds: F:D.19, F:W.53, F:T.79, F:Y.80, F:F.159, F:S.161, B:N.218, B:R.280 Hydrophobic interactions: B:F.257 Water bridges: B:R.280 pi-Stacking: B:F.257, B:F.257 1DA.8: 20 residues within 4Å: Chain C: F.216, N.218, F.257, A.279, R.280, N.281, A.282, A.283 Chain E: D.19, L.20, W.53, T.79, Y.80, P.81, T.83, T.158, F.159, Y.160, S.161, R.162 15 PLIP interactions: 9 interactions with chain E, 6 interactions with chain C Hydrogen bonds: E:D.19, E:D.19, E:W.53, E:T.79, E:Y.80, E:F.159, E:S.161, C:N.218, C:N.218 pi-Stacking: E:W.53, E:W.53, C:F.257, C:F.257 Hydrophobic interactions: C:F.257 Water bridges: C:R.280 1DA.11: 20 residues within 4Å: Chain B: D.19, L.20, W.53, T.79, Y.80, P.81, T.83, T.158, F.159, Y.160, S.161, R.162 Chain D: F.216, N.218, F.257, A.279, R.280, N.281, A.282, A.283 12 PLIP interactions: 6 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:F.257 Hydrogen bonds: D:N.218, D:R.280, B:D.19, B:W.53, B:T.79, B:Y.80, B:F.159, B:S.161 Water bridges: D:R.280 pi-Stacking: D:F.257, D:F.257 1DA.15: 20 residues within 4Å: Chain A: D.19, L.20, W.53, T.79, Y.80, P.81, T.83, T.158, F.159, Y.160, S.161, R.162 Chain E: F.216, N.218, F.257, A.279, R.280, N.281, A.282, A.283 15 PLIP interactions: 9 interactions with chain A, 6 interactions with chain E Hydrogen bonds: A:D.19, A:D.19, A:W.53, A:T.79, A:Y.80, A:F.159, A:S.161, E:N.218, E:N.218 pi-Stacking: A:W.53, A:W.53, E:F.257, E:F.257 Hydrophobic interactions: E:F.257 Water bridges: E:R.280 1DA.18: 20 residues within 4Å: Chain D: D.19, L.20, W.53, T.79, Y.80, P.81, T.83, T.158, F.159, Y.160, S.161, R.162 Chain F: F.216, N.218, F.257, A.279, R.280, N.281, A.282, A.283 12 PLIP interactions: 6 interactions with chain F, 6 interactions with chain D Hydrophobic interactions: F:F.257 Hydrogen bonds: F:N.218, F:R.280, D:D.19, D:W.53, D:T.79, D:Y.80, D:F.159, D:S.161 Water bridges: F:R.280 pi-Stacking: F:F.257, F:F.257

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

CL.2: 5 residues within 4Å: Chain A: Y.80, P.81, A.82, P.125, N.127 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain B: Y.80, P.81, A.82, T.87, P.125, N.127 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain B: V.44 Chain F: K.31, H.35, V.43 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain C: Y.80, P.81, A.82, P.125, N.127 Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain D: Y.80, P.81, A.82, T.87, P.125, N.127 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain B: K.31, H.35, V.43 Chain D: V.44 Ligand excluded by PLIP CL.16: 5 residues within 4Å: Chain E: Y.80, P.81, A.82, P.125, N.127 Ligand excluded by PLIP CL.19: 6 residues within 4Å: Chain F: Y.80, P.81, A.82, T.87, P.125, N.127 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain D: K.31, H.35, V.43 Chain F: V.44 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: E.71, G.72, R.93, G.118, S.119, Y.120, I.121 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.72, A:R.93, A:R.93, A:S.119, A:S.119 GOL.7: 10 residues within 4Å: Chain B: G.21, T.22, V.27, A.28, K.31, D.45, H.48 Chain D: D.45, V.46, C.47 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:K.31 Water bridges: B:D.45, D:D.45 GOL.10: 7 residues within 4Å: Chain C: E.71, G.72, R.93, G.118, S.119, Y.120, I.121 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.72, C:R.93, C:R.93, C:S.119, C:S.119 GOL.14: 10 residues within 4Å: Chain D: G.21, T.22, V.27, A.28, K.31, D.45, H.48 Chain F: D.45, V.46, C.47 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:K.31 Water bridges: D:D.45, F:D.45 GOL.17: 7 residues within 4Å: Chain E: E.71, G.72, R.93, G.118, S.119, Y.120, I.121 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:G.72, E:R.93, E:R.93, E:S.119, E:S.119 GOL.21: 10 residues within 4Å: Chain B: D.45, V.46, C.47 Chain F: G.21, T.22, V.27, A.28, K.31, D.45, H.48 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:K.31 Water bridges: F:D.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, H. et al., Identification of fluorinases from Streptomyces sp MA37, Norcardia brasiliensis, and Actinoplanes sp N902-109 by genome mining. Chembiochem (2014)

Release Date

2016-08-24

Peptides

Fluorinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Fluorinase