SMTL ID : 1yqn.1

E. coli ispF double mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.11 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.10, H.12, H.44 Ligands: CDP.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.10, A:D.10, A:H.12, A:H.44 ZN.5: 4 residues within 4Å: Chain B: D.10, H.12, H.44 Ligands: CDP.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.10, B:D.10, B:H.12, B:H.44 ZN.9: 4 residues within 4Å: Chain C: D.10, H.12, H.44 Ligands: CDP.11 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.10, C:D.10, C:H.12, C:H.44

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 2 residues within 4Å: Chain A: E.137 Ligands: CDP.11 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.137, H2O.1, H2O.1, H2O.1 MN.6: 2 residues within 4Å: Chain B: E.137 Ligands: CDP.3 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.137, H2O.2, H2O.2, H2O.2 MN.10: 2 residues within 4Å: Chain C: E.137 Ligands: CDP.7 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.137, H2O.3, H2O.3, H2O.3

3 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.3: 18 residues within 4Å: Chain A: D.10, H.12, H.44, D.58, I.59, G.60, D.65 Chain B: A.102, P.105, K.106, M.107, L.108, A.133, T.134, T.135, E.137 Ligands: ZN.1, MN.6 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.133, B:T.135 Hydrogen bonds: B:A.102, B:M.107, B:L.108, B:T.135, A:D.58, A:G.60 Salt bridges: A:H.12, A:H.44 CDP.7: 18 residues within 4Å: Chain B: D.10, H.12, H.44, D.58, I.59, G.60, D.65 Chain C: A.102, P.105, K.106, M.107, L.108, A.133, T.134, T.135, E.137 Ligands: ZN.5, MN.10 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:A.133, C:T.135 Hydrogen bonds: C:A.102, C:M.107, C:L.108, C:T.135, B:D.58, B:G.60 Salt bridges: B:H.12, B:H.44 CDP.11: 18 residues within 4Å: Chain A: A.102, P.105, K.106, M.107, L.108, A.133, T.134, T.135, E.137 Chain C: D.10, H.12, H.44, D.58, I.59, G.60, D.65 Ligands: MN.2, ZN.9 11 PLIP interactions: 4 interactions with chain C, 7 interactions with chain A Hydrogen bonds: C:D.58, C:G.60, A:A.102, A:M.107, A:L.108, A:T.134, A:T.135 Salt bridges: C:H.12, C:H.44 Hydrophobic interactions: A:A.133, A:T.135

3 x GPP: GERANYL DIPHOSPHATE(Non-covalent)

GPP.4: 14 residues within 4Å: Chain A: F.9, G.140, F.141, E.151 Chain B: F.9, G.140, F.141, E.151 Chain C: F.9, G.140, F.141, E.151 Ligands: GPP.8, GPP.12 9 PLIP interactions: 2 interactions with chain C, 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: C:F.141, A:F.141, B:F.141 Water bridges: C:T.142, A:T.142 Hydrophobic interactions: A:F.9, A:F.9, A:F.141, B:F.9 GPP.8: 14 residues within 4Å: Chain A: F.9, G.140, F.141, E.151 Chain B: F.9, G.140, F.141, E.151 Chain C: F.9, G.140, F.141, E.151 Ligands: GPP.4, GPP.12 9 PLIP interactions: 2 interactions with chain C, 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: C:F.9, B:F.9, B:F.9, B:F.141 Hydrogen bonds: C:F.141, B:F.141, A:F.141 Water bridges: B:T.142, A:T.142 GPP.12: 14 residues within 4Å: Chain A: F.9, G.140, F.141, E.151 Chain B: F.9, G.140, F.141, E.151 Chain C: F.9, G.140, F.141, E.151 Ligands: GPP.4, GPP.8 9 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: C:F.9, C:F.9, C:F.141, A:F.9 Hydrogen bonds: C:F.141, A:F.141, B:F.141 Water bridges: C:T.142, B:T.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sgraja, T. et al., A double mutation of Escherichia coli2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase disrupts six hydrogen bonds with, yet fails to prevent binding of, an isoprenoid diphosphate. Acta Crystallogr.,Sect.F (2005)

Release Date

2005-07-12

Peptides

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase