SMTL ID : 1w57.1

Structure of the Bifunctional IspDF from Campylobacter jejuni containing Zn

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.09 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.217, H.219, H.243, H.251 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.217, A:H.219, A:H.251, H2O.3 ZN.5: 4 residues within 4Å: Chain B: D.217, H.219, H.243, H.251 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.217, B:H.219, B:H.251, H2O.5 ZN.9: 4 residues within 4Å: Chain C: D.217, H.219, H.243, H.251 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.217, C:H.219, C:H.251, H2O.7 ZN.13: 4 residues within 4Å: Chain D: D.217, H.219, H.243, H.251 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.217, D:H.219, D:H.251, H2O.9 ZN.17: 4 residues within 4Å: Chain E: D.217, H.219, H.243, H.251 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.217, E:H.219, E:H.251, H2O.11 ZN.21: 4 residues within 4Å: Chain F: D.217, H.219, H.243, H.251 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.217, F:H.219, F:H.251, H2O.14

12 x C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C5P.2: 16 residues within 4Å: Chain A: D.217, D.265, I.266, G.267, E.268, D.272 Chain B: A.309, P.312, K.313, L.314, K.315, K.318, A.340, T.341, T.342, E.344 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:T.342 Hydrogen bonds: B:A.309, B:L.314, B:K.315, B:K.318, B:T.342, B:E.344, A:D.217, A:D.265, A:G.267, A:D.272 C5P.3: 16 residues within 4Å: Chain A: L.9, A.10, A.11, G.12, Q.24, T.53, G.73, D.74, T.75, R.76, S.79, D.96, V.97, A.98, K.191 Chain D: R.139 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:A.11, A:Q.24, A:T.53, A:G.73, A:S.79, A:D.96, A:V.97, A:A.98 Salt bridges: A:K.191, D:R.139 C5P.6: 16 residues within 4Å: Chain B: D.217, D.265, I.266, G.267, E.268, D.272 Chain C: A.309, P.312, K.313, L.314, K.315, K.318, A.340, T.341, T.342, E.344 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain C Hydrogen bonds: B:D.217, B:D.265, B:G.267, B:D.272, C:A.309, C:L.314, C:K.315, C:K.318, C:T.342, C:E.344 Hydrophobic interactions: C:T.342 C5P.7: 16 residues within 4Å: Chain B: L.9, A.10, A.11, G.12, Q.24, T.53, G.73, D.74, T.75, R.76, S.79, D.96, V.97, A.98, K.191 Chain F: R.139 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:A.11, B:Q.24, B:T.53, B:G.73, B:S.79, B:D.96, B:V.97, B:A.98 Salt bridges: B:K.191, F:R.139 C5P.10: 16 residues within 4Å: Chain A: A.309, P.312, K.313, L.314, K.315, K.318, A.340, T.341, T.342, E.344 Chain C: D.217, D.265, I.266, G.267, E.268, D.272 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:T.342 Hydrogen bonds: A:A.309, A:L.314, A:K.315, A:K.318, A:T.342, A:E.344, C:D.217, C:D.265, C:G.267, C:D.272 C5P.11: 16 residues within 4Å: Chain C: L.9, A.10, A.11, G.12, Q.24, T.53, G.73, D.74, T.75, R.76, S.79, D.96, V.97, A.98, K.191 Chain E: R.139 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain E Hydrogen bonds: C:A.11, C:Q.24, C:T.53, C:G.73, C:S.79, C:D.96, C:V.97, C:A.98 Salt bridges: C:K.191, E:R.139 C5P.14: 16 residues within 4Å: Chain D: D.217, D.265, I.266, G.267, E.268, D.272 Chain E: A.309, P.312, K.313, L.314, K.315, K.318, A.340, T.341, T.342, E.344 13 PLIP interactions: 10 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:T.342 Hydrogen bonds: E:A.309, E:L.314, E:K.315, E:K.318, E:T.341, E:T.342, E:E.344, E:E.344, D:D.217, D:D.265, D:G.267 Water bridges: E:T.342 C5P.15: 16 residues within 4Å: Chain A: R.139 Chain D: L.9, A.10, A.11, G.12, Q.24, T.53, G.73, D.74, T.75, R.76, S.79, D.96, V.97, A.98, K.191 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:A.11, D:Q.24, D:G.73, D:S.79, D:V.97, D:A.98 Salt bridges: D:K.191, A:R.139 C5P.18: 16 residues within 4Å: Chain E: D.217, D.265, I.266, G.267, E.268, D.272 Chain F: A.309, P.312, K.313, L.314, K.315, K.318, A.340, T.341, T.342, E.344 13 PLIP interactions: 10 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:T.342 Hydrogen bonds: F:A.309, F:L.314, F:K.315, F:K.318, F:T.341, F:T.342, F:E.344, F:E.344, E:D.217, E:D.265, E:G.267 Water bridges: F:T.342 C5P.19: 16 residues within 4Å: Chain C: R.139 Chain E: L.9, A.10, A.11, G.12, Q.24, T.53, G.73, D.74, T.75, R.76, S.79, D.96, V.97, A.98, K.191 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:A.11, E:Q.24, E:G.73, E:S.79, E:V.97, E:A.98 Salt bridges: E:K.191, C:R.139 C5P.22: 16 residues within 4Å: Chain D: A.309, P.312, K.313, L.314, K.315, K.318, A.340, T.341, T.342, E.344 Chain F: D.217, D.265, I.266, G.267, E.268, D.272 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain F Hydrophobic interactions: D:T.342 Hydrogen bonds: D:A.309, D:L.314, D:K.315, D:K.318, D:T.341, D:T.342, D:E.344, D:E.344, F:D.217, F:D.265, F:G.267 Water bridges: D:T.342 C5P.23: 16 residues within 4Å: Chain B: R.139 Chain F: L.9, A.10, A.11, G.12, Q.24, T.53, G.73, D.74, T.75, R.76, S.79, D.96, V.97, A.98, K.191 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain F Salt bridges: B:R.139, F:K.191 Hydrogen bonds: F:A.11, F:Q.24, F:G.73, F:S.79, F:V.97, F:A.98

6 x GPP: GERANYL DIPHOSPHATE(Non-covalent)

GPP.4: 16 residues within 4Å: Chain A: F.216, M.308, G.347, F.348, R.351 Chain B: F.216, M.308, G.347, F.348, I.349, R.351 Chain C: G.347, F.348, R.351 Ligands: GPP.8, GPP.12 14 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: B:F.216, B:F.348, B:I.349, A:F.216 Hydrogen bonds: B:G.347, B:F.348, A:F.348, C:F.348 Water bridges: B:I.349, A:I.349, C:I.349 Salt bridges: B:R.351, A:R.351, C:R.351 GPP.8: 16 residues within 4Å: Chain A: G.347, F.348, R.351 Chain B: F.216, M.308, G.347, F.348, R.351 Chain C: F.216, M.308, G.347, F.348, I.349, R.351 Ligands: GPP.4, GPP.12 14 PLIP interactions: 4 interactions with chain B, 7 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: B:F.216, C:F.216, C:F.348, C:I.349 Hydrogen bonds: B:F.348, C:G.347, C:F.348, A:F.348 Water bridges: B:I.349, C:I.349, A:I.349 Salt bridges: B:R.351, C:R.351, A:R.351 GPP.12: 16 residues within 4Å: Chain A: F.216, M.308, G.347, F.348, I.349, R.351 Chain B: G.347, F.348, R.351 Chain C: F.216, M.308, G.347, F.348, R.351 Ligands: GPP.4, GPP.8 14 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: A:F.216, A:F.348, A:I.349, C:F.216 Hydrogen bonds: A:G.347, A:F.348, B:F.348, C:F.348 Water bridges: A:I.349, B:I.349, C:I.349 Salt bridges: A:R.351, B:R.351, C:R.351 GPP.16: 16 residues within 4Å: Chain D: F.216, M.308, G.347, F.348, R.351 Chain E: F.216, M.308, G.347, F.348, I.349, R.351 Chain F: G.347, F.348, R.351 Ligands: GPP.20, GPP.24 14 PLIP interactions: 3 interactions with chain F, 4 interactions with chain D, 7 interactions with chain E Hydrogen bonds: F:F.348, D:F.348, E:G.347, E:F.348 Water bridges: F:I.349, D:I.349, E:I.349 Salt bridges: F:R.351, D:R.351, E:R.351 Hydrophobic interactions: D:F.216, E:F.216, E:F.348, E:I.349 GPP.20: 16 residues within 4Å: Chain D: G.347, F.348, R.351 Chain E: F.216, M.308, G.347, F.348, R.351 Chain F: F.216, M.308, G.347, F.348, I.349, R.351 Ligands: GPP.16, GPP.24 14 PLIP interactions: 7 interactions with chain F, 3 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: F:F.216, F:F.348, F:I.349, E:F.216 Hydrogen bonds: F:G.347, F:F.348, D:F.348, E:F.348 Water bridges: F:I.349, D:I.349, E:I.349 Salt bridges: F:R.351, D:R.351, E:R.351 GPP.24: 16 residues within 4Å: Chain D: F.216, M.308, G.347, F.348, I.349, R.351 Chain E: G.347, F.348, R.351 Chain F: F.216, M.308, G.347, F.348, R.351 Ligands: GPP.16, GPP.20 14 PLIP interactions: 4 interactions with chain F, 7 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: F:F.216, D:F.216, D:F.348, D:I.349 Hydrogen bonds: F:F.348, D:G.347, D:F.348, E:F.348 Water bridges: F:I.349, D:I.349, E:I.349 Salt bridges: F:R.351, D:R.351, E:R.351

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gabrielsen, M. et al., Hexameric Assembly of the Bifunctional Methylerythritol 2,4-Cyclodiphosphate Synthase and Protein-Protein Associations in the Deoxy-Xylulose-Dependent Pathway of Isoprenoid Precursor Biosynthesis. J.Biol.Chem. (2004)

Release Date

2004-10-04

Peptides

ISPD/ISPF BIFUNCTIONAL ENZYME: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

ISPD/ISPF BIFUNCTIONAL ENZYME

Related Entries With Identical Sequence