SMTL ID : 1zcc.1

Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens str.C58

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-hexamer

Ligands

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 5 residues within 4Å: Chain A: Y.106, E.108, M.153, E.175 Ligands: SO4.2 No protein-ligand interaction detected (PLIP) ACT.3: 6 residues within 4Å: Chain B: Y.106, E.108, F.135, M.153, E.175 Ligands: SO4.4 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.135 ACT.5: 7 residues within 4Å: Chain C: E.34, Y.106, E.108, F.135, M.153, E.175 Ligands: SO4.6 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.135 Hydrogen bonds: C:E.34, C:E.175 ACT.7: 6 residues within 4Å: Chain D: Y.106, E.108, F.135, M.153, E.175, N.221 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.135 Hydrogen bonds: D:Y.106 ACT.9: 9 residues within 4Å: Chain E: H.7, E.34, Y.106, E.108, F.135, M.153, E.175, N.221 Ligands: SO4.10 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.135 Hydrogen bonds: E:Y.106, E:E.175 ACT.11: 8 residues within 4Å: Chain F: E.34, Y.106, E.108, F.135, M.153, E.175, N.221 Ligands: SO4.12 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:F.135 Hydrogen bonds: F:Y.106, F:E.175

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

SO4.2: 8 residues within 4Å: Chain A: H.7, R.8, H.49, E.108, K.110, F.135, Y.200 Ligands: ACT.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.200 Salt bridges: A:H.7, A:R.8, A:H.49, A:K.110 SO4.4: 5 residues within 4Å: Chain B: H.7, R.8, H.49, E.108 Ligands: ACT.3 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.8 Water bridges: B:E.34 Salt bridges: B:H.7, B:H.49, B:K.110 SO4.6: 5 residues within 4Å: Chain C: H.7, R.8, H.49, K.110 Ligands: ACT.5 4 PLIP interactions: 4 interactions with chain C Salt bridges: C:H.7, C:R.8, C:H.49, C:K.110 SO4.8: 6 residues within 4Å: Chain D: H.7, R.8, H.49, E.108, K.110, F.135 3 PLIP interactions: 3 interactions with chain D Salt bridges: D:R.8, D:H.49, D:K.110 SO4.10: 5 residues within 4Å: Chain E: H.7, R.8, H.49, Y.200 Ligands: ACT.9 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:H.7, E:R.8 SO4.12: 5 residues within 4Å: Chain F: H.7, R.8, E.108, Y.200 Ligands: ACT.11 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:Y.200 Salt bridges: F:H.7, F:R.8, F:K.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rao, K.N. et al., Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens by SAD with a large asymmetric unit. Proteins (2006)

Release Date

2005-05-03

Peptides

glycerophosphodiester phosphodiesterase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

glycerophosphodiester phosphodiesterase