SMTL ID : 2cbx.1

X-ray crystal structure of 5'-fluorodeoxyadenosine synthase from Streptomyces cattleya complexed with beta-D-erythrofuranosyl- adenosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

6 x CC5: BETA-D-ERYTHROFURANOSYL-ADENOSINE(Non-covalent)

CC5.1: 18 residues within 4Å: Chain A: D.16, L.17, W.50, T.76, Y.77, P.78, T.80, T.155, S.158 Chain B: F.213, N.215, F.254, A.276, R.277, N.278, A.279, A.280 Ligands: GOL.5 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.215, B:R.277, B:A.279, A:D.16, A:W.50, A:Y.77, A:S.158 Water bridges: B:R.277 pi-Stacking: B:F.254, B:F.254 CC5.7: 17 residues within 4Å: Chain B: D.16, L.17, W.50, T.76, Y.77, P.78, T.80, T.155, S.158 Chain C: F.213, N.215, F.254, A.276, R.277, N.278, A.279, A.280 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:D.16, B:W.50, B:Y.77, B:S.158, C:N.215, C:R.277, C:A.279 Water bridges: C:R.277 pi-Stacking: C:F.254, C:F.254 CC5.9: 17 residues within 4Å: Chain A: F.213, N.215, F.254, A.276, R.277, N.278, A.279 Chain C: D.16, L.17, W.50, T.76, Y.77, P.78, T.80, T.155, S.158 Ligands: GOL.4 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:D.16, C:W.50, C:Y.77, C:S.158, A:N.215, A:R.277, A:A.279 Water bridges: A:R.277 pi-Stacking: A:F.254, A:F.254 CC5.13: 18 residues within 4Å: Chain D: D.16, L.17, W.50, T.76, Y.77, P.78, T.80, T.155, S.158 Chain E: F.213, N.215, F.254, A.276, R.277, N.278, A.279, A.280 Ligands: GOL.17 11 PLIP interactions: 6 interactions with chain E, 5 interactions with chain D Hydrogen bonds: E:N.215, E:R.277, E:A.279, D:D.16, D:W.50, D:T.76, D:Y.77, D:S.158 Water bridges: E:R.277 pi-Stacking: E:F.254, E:F.254 CC5.19: 17 residues within 4Å: Chain E: D.16, L.17, W.50, T.76, Y.77, P.78, T.80, T.155, S.158 Chain F: F.213, N.215, F.254, A.276, R.277, N.278, A.279, A.280 11 PLIP interactions: 5 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:D.16, E:W.50, E:T.76, E:Y.77, E:S.158, F:N.215, F:R.277, F:A.279 Water bridges: F:R.277 pi-Stacking: F:F.254, F:F.254 CC5.21: 17 residues within 4Å: Chain D: F.213, N.215, F.254, A.276, R.277, N.278, A.279 Chain F: D.16, L.17, W.50, T.76, Y.77, P.78, T.80, T.155, S.158 Ligands: GOL.16 11 PLIP interactions: 5 interactions with chain F, 6 interactions with chain D Hydrogen bonds: F:D.16, F:W.50, F:T.76, F:Y.77, F:S.158, D:N.215, D:R.277, D:A.279 Water bridges: D:R.277 pi-Stacking: D:F.254, D:F.254

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: T.19, V.24, K.28, D.42 Chain B: D.42, V.43 Ligand excluded by PLIP GOL.3: 2 residues within 4Å: Chain A: Y.136, L.137 Ligand excluded by PLIP GOL.4: 10 residues within 4Å: Chain A: D.210, F.213, W.217, S.269, R.270 Chain C: D.21, S.23, T.155, F.156 Ligands: CC5.9 Ligand excluded by PLIP GOL.5: 7 residues within 4Å: Chain A: L.17, S.23, T.155, F.156 Chain B: F.213, S.269 Ligands: CC5.1 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: G.69, V.71, I.118, L.169, A.170, G.172 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain B: T.19, V.24, K.28, D.42, H.45 Chain C: D.42, V.43 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain A: D.42, V.43 Chain C: T.19, V.24, K.28, D.42, H.45 Ligand excluded by PLIP GOL.11: 2 residues within 4Å: Chain C: Y.136, L.137 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain C: D.241 Chain E: R.277, P.285, Y.286 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain D: T.19, V.24, K.28, D.42 Chain E: D.42, V.43 Ligand excluded by PLIP GOL.15: 2 residues within 4Å: Chain D: Y.136, L.137 Ligand excluded by PLIP GOL.16: 10 residues within 4Å: Chain D: D.210, F.213, W.217, S.269, R.270 Chain F: D.21, S.23, T.155, F.156 Ligands: CC5.21 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain D: L.17, S.23, T.155, F.156 Chain E: F.213, S.269 Ligands: CC5.13 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain D: G.69, V.71, I.118, L.169, A.170, G.172 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain E: T.19, V.24, K.28, D.42, H.45 Chain F: D.42, V.43 Ligand excluded by PLIP GOL.22: 7 residues within 4Å: Chain D: D.42, V.43 Chain F: T.19, V.24, K.28, D.42, H.45 Ligand excluded by PLIP GOL.23: 2 residues within 4Å: Chain F: Y.136, L.137 Ligand excluded by PLIP GOL.24: 4 residues within 4Å: Chain B: R.277, P.285, Y.286 Chain F: D.241 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cobb, S.L. et al., Substrate specificity in enzymatic fluorination. The fluorinase from Streptomyces cattleya accepts 2'-deoxyadenosine substrates. Org. Biomol. Chem. (2006)

Release Date

2007-03-06

Peptides

5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE

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