SMTL ID : 1rqr.1 (1 other biounit)

Crystal structure and mechanism of a bacterial fluorinating enzyme, product complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.67 Å

Oligo State

homo-hexamer

Ligands

6 x 5FD: 5'-FLUORO-5'-DEOXYADENOSINE(Non-covalent)

5FD.1: 17 residues within 4Å: Chain A: D.16, 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, N.278, A.279 Ligands: MET.2 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:D.16, A:D.16, A:Y.77, A:S.158, B:N.215, B:R.277, B:A.279 Water bridges: B:R.277 pi-Stacking: B:F.254, B:F.254 5FD.3: 19 residues within 4Å: Chain B: D.16, W.50, T.76, Y.77, P.78, T.80, T.155, F.156, Y.157, S.158 Chain C: F.213, N.215, F.254, A.276, R.277, N.278, A.279, A.280 Ligands: MET.4 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:D.16, B:D.16, 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 5FD.5: 17 residues within 4Å: Chain A: F.213, N.215, F.254, R.277, N.278, A.279 Chain C: D.16, W.50, T.76, Y.77, P.78, T.80, T.155, F.156, Y.157, S.158 Ligands: MET.6 10 PLIP interactions: 4 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:D.16, C:D.16, 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 5FD.7: 17 residues within 4Å: Chain D: D.16, 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, N.278, A.279 Ligands: MET.8 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:D.16, D:T.76, D:Y.77, D:S.158 Water bridges: E:R.277 pi-Stacking: E:F.254, E:F.254 5FD.9: 19 residues within 4Å: Chain E: D.16, W.50, T.76, Y.77, P.78, T.80, T.155, F.156, Y.157, S.158 Chain F: F.213, N.215, F.254, A.276, R.277, N.278, A.279, A.280 Ligands: MET.10 11 PLIP interactions: 5 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:D.16, E:D.16, 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 5FD.11: 17 residues within 4Å: Chain D: F.213, N.215, F.254, R.277, N.278, A.279 Chain F: D.16, W.50, T.76, Y.77, P.78, T.80, T.155, F.156, Y.157, S.158 Ligands: MET.12 11 PLIP interactions: 6 interactions with chain D, 5 interactions with chain F Hydrogen bonds: D:N.215, D:R.277, D:A.279, F:D.16, F:D.16, F:T.76, F:Y.77, F:S.158 Water bridges: D:R.277 pi-Stacking: D:F.254, D:F.254

6 x MET: METHIONINE(Non-covalent)

MET.2: 10 residues within 4Å: Chain A: L.17, D.21, S.23, T.155 Chain B: D.210, F.213, W.217, S.269, R.270 Ligands: 5FD.1 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.17 Hydrogen bonds: A:S.23, B:D.210, B:S.269 Water bridges: A:T.155, B:D.210, B:S.269 Salt bridges: B:R.270 MET.4: 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: 5FD.3 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.6: 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: 5FD.5 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:S.23, A:D.210, A:S.269 Water bridges: C:T.155, A:S.269 Hydrophobic interactions: A:F.213 Salt bridges: A:R.270 MET.8: 10 residues within 4Å: Chain D: L.17, D.21, S.23, T.155 Chain E: D.210, F.213, W.217, S.269, R.270 Ligands: 5FD.7 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:L.17 Hydrogen bonds: D:S.23, E:D.210, E:S.269 Water bridges: D:D.21, D:T.155, E:S.269 Salt bridges: E:R.270 MET.10: 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: 5FD.9 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.12: 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: 5FD.11 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:F.213 Hydrogen bonds: D:D.210, D:S.269, F:S.23 Water bridges: D:S.269, F:T.155 Salt bridges: D:R.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, C. et al., Crystal structure and mechanism of a bacterial fluorinating enzyme. Nature (2004)

Release Date

2004-03-02

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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