SMTL ID : 2c5b.1

X-ray crystal structure of 5'-fluorodeoxyadenosine synthase from Streptomyces cattleya complexed with 2'deoxy-5'deoxy-fluoroadenosine.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

6 x MET: METHIONINE(Non-covalent)

MET.1: 12 residues within 4Å: Chain A: D.21, S.23, T.155, F.156 Chain B: D.210, F.213, N.215, W.217, F.254, S.269, R.270 Ligands: 5F1.2 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.210, B:S.269, B:S.269, A:S.23 Water bridges: B:D.210, B:D.210, A:T.155 Salt bridges: B:R.270 MET.3: 11 residues within 4Å: Chain B: D.21, S.23, T.155, F.156 Chain C: D.210, F.213, W.217, F.254, S.269, R.270 Ligands: 5F1.4 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:S.23, C:D.210, C:S.269 Water bridges: C:D.210 Salt bridges: C:R.270 MET.5: 11 residues within 4Å: Chain A: D.210, F.213, N.215, W.217, S.269, R.270 Chain C: D.21, S.23, T.155, F.156 Ligands: 5F1.6 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:S.23, C:T.155, A:D.210, A:S.269 Salt bridges: A:R.270 MET.7: 12 residues within 4Å: Chain D: D.21, S.23, T.155, F.156 Chain E: D.210, F.213, N.215, W.217, F.254, S.269, R.270 Ligands: 5F1.8 8 PLIP interactions: 3 interactions with chain D, 1 Ligand-Ligand interactions, 4 interactions with chain E Hydrogen bonds: D:D.21, D:S.23, E:D.210, E:S.269, E:S.269 Water bridges: D:T.155, M.7 Salt bridges: E:R.270 MET.9: 11 residues within 4Å: Chain E: D.21, S.23, T.155, F.156 Chain F: D.210, F.213, W.217, F.254, S.269, R.270 Ligands: 5F1.10 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:D.210, F:S.269, E:S.23 Salt bridges: F:R.270 Water bridges: E:D.21 MET.11: 11 residues within 4Å: Chain D: D.210, F.213, N.215, W.217, S.269, R.270 Chain F: D.21, S.23, T.155, F.156 Ligands: 5F1.12 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain D Hydrogen bonds: F:S.23, F:T.155, F:T.155, D:D.210, D:S.269 Salt bridges: D:R.270

6 x 5F1: 5'-FLUORO-2',5'-DIDEOXYADENOSINE(Non-covalent)

5F1.2: 17 residues within 4Å: Chain A: D.16, L.17, W.50, T.76, Y.77, P.78, T.80, T.155, F.156, Y.157, S.158 Chain B: F.213, N.215, F.254, R.277, A.279 Ligands: MET.1 14 PLIP interactions: 7 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:D.16, A:Y.77, A:S.158, B:N.215, B:R.277, B:A.279 pi-Stacking: A:W.50, A:W.50, A:W.50, B:F.254, B:F.254 Halogen bonds: A:T.80 Hydrophobic interactions: B:F.213 Water bridges: B:R.277 5F1.4: 17 residues within 4Å: Chain B: D.16, L.17, W.50, Y.77, P.78, T.80, T.155, F.156, Y.157, S.158 Chain C: F.213, N.215, F.254, R.277, N.278, A.279 Ligands: MET.3 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:D.16, B:Y.77, B:S.158, C:N.215, C:R.277, C:A.279 pi-Stacking: B:W.50, B:W.50, B:W.50, C:F.254 Hydrophobic interactions: C:F.213 Water bridges: C:R.277 5F1.6: 17 residues within 4Å: Chain A: F.213, N.215, F.254, R.277, N.278, A.279, A.280 Chain C: D.16, W.50, Y.77, P.78, T.80, T.155, F.156, Y.157, S.158 Ligands: MET.5 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:F.213 Hydrogen bonds: A:N.215, A:R.277, A:A.279, C:D.16, C:Y.77, C:S.158 pi-Stacking: A:F.254, A:F.254, C:W.50, C:W.50, C:W.50 5F1.8: 17 residues within 4Å: Chain D: D.16, L.17, W.50, T.76, Y.77, P.78, T.80, T.155, F.156, Y.157, S.158 Chain E: F.213, N.215, F.254, R.277, A.279 Ligands: MET.7 14 PLIP interactions: 7 interactions with chain E, 7 interactions with chain D Hydrophobic interactions: E:F.213 Hydrogen bonds: E:N.215, E:R.277, E:A.279, D:D.16, D:Y.77, D:S.158 Water bridges: E:R.277 pi-Stacking: E:F.254, E:F.254, D:W.50, D:W.50, D:W.50 Halogen bonds: D:T.80 5F1.10: 17 residues within 4Å: Chain E: D.16, L.17, W.50, Y.77, P.78, T.80, T.155, F.156, Y.157, S.158 Chain F: F.213, N.215, F.254, R.277, N.278, A.279 Ligands: MET.9 12 PLIP interactions: 6 interactions with chain F, 6 interactions with chain E Hydrophobic interactions: F:F.213 Hydrogen bonds: F:N.215, F:R.277, F:A.279, E:D.16, E:Y.77, E:S.158 Water bridges: F:R.277 pi-Stacking: F:F.254, E:W.50, E:W.50, E:W.50 5F1.12: 17 residues within 4Å: Chain D: F.213, N.215, F.254, R.277, N.278, A.279, A.280 Chain F: D.16, W.50, Y.77, P.78, T.80, T.155, F.156, Y.157, S.158 Ligands: MET.11 12 PLIP interactions: 6 interactions with chain D, 6 interactions with chain F Hydrophobic interactions: D:F.213 Hydrogen bonds: D:N.215, D:R.277, D:A.279, F:D.16, F:Y.77, F:S.158 pi-Stacking: D:F.254, D:F.254, F:W.50, F:W.50, F:W.50

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

2007-02-20

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

Related Entries With Identical Sequence