SMTL ID : 1su1.1

Structural and biochemical characterization of Yfce, a phosphoesterase from E. coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: D.33, D.61, N.97, H.129, H.151 Ligands: ZN.2, SO4.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.61, A:H.129, A:H.151 ZN.2: 6 residues within 4Å: Chain A: D.33, H.35, D.61, H.153 Ligands: ZN.1, SO4.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.33, A:H.35, A:H.153 ZN.4: 7 residues within 4Å: Chain B: D.33, D.61, N.97, H.129, H.151 Ligands: ZN.5, SO4.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.61, B:H.129, B:H.151 ZN.5: 6 residues within 4Å: Chain B: D.33, H.35, D.61, H.153 Ligands: ZN.4, SO4.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.33, B:H.35, B:H.153 ZN.7: 7 residues within 4Å: Chain C: D.33, D.61, N.97, H.129, H.151 Ligands: ZN.8, SO4.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.61, C:H.129, C:H.151 ZN.8: 6 residues within 4Å: Chain C: D.33, H.35, D.61, H.153 Ligands: ZN.7, SO4.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.33, C:H.35, C:D.61, C:H.153 ZN.11: 6 residues within 4Å: Chain D: D.33, H.35, D.61, H.153 Ligands: ZN.12, SO4.13 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.33, D:H.35, D:D.61, D:H.153 ZN.12: 7 residues within 4Å: Chain D: D.33, D.61, N.97, H.129, H.151 Ligands: ZN.11, SO4.13 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.61, D:H.129, D:H.151

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 11 residues within 4Å: Chain A: D.33, H.35, D.61, R.68, N.69, N.97, C.98, H.151, H.153 Ligands: ZN.1, ZN.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.61, A:N.69, A:N.97 Water bridges: A:N.69 Salt bridges: A:H.35, A:R.68, A:H.151, A:H.153 SO4.6: 10 residues within 4Å: Chain B: D.33, H.35, D.61, N.69, N.97, C.98, H.151, H.153 Ligands: ZN.4, ZN.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.69, B:N.97, B:H.151 Water bridges: B:G.66, B:N.69, B:K.175 Salt bridges: B:H.35, B:H.151, B:H.153 SO4.9: 10 residues within 4Å: Chain C: D.33, H.35, D.61, N.69, N.97, C.98, H.151, H.153 Ligands: ZN.7, ZN.8 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.97 Salt bridges: C:H.35, C:H.151, C:H.153, C:K.175 SO4.10: 4 residues within 4Å: Chain C: R.95, P.114, L.132 Ligands: SO4.14 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.95 SO4.13: 11 residues within 4Å: Chain D: D.33, H.35, D.61, N.69, N.97, C.98, H.151, H.153, K.175 Ligands: ZN.11, ZN.12 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.69, D:N.97, D:N.97 Salt bridges: D:H.35, D:H.151, D:H.153, D:K.175 SO4.14: 3 residues within 4Å: Chain D: R.95, P.114 Ligands: SO4.10 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, D.J. et al., Structural and biochemical characterization of a novel Mn2+-dependent phosphodiesterase encoded by the yfcE gene. Protein Sci. (2007)

Release Date

2004-08-17

Peptides

Hypothetical protein yfcE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Hypothetical protein yfcE