SMTL ID : 2gzl.1

Structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with a CDP derived fluorescent inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 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: 2AA.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.10, A:H.12, A:H.44 ZN.4: 4 residues within 4Å: Chain B: D.10, H.12, H.44 Ligands: 2AA.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.10, B:H.12, B:H.44 ZN.7: 4 residues within 4Å: Chain C: D.10, H.12, H.44 Ligands: 2AA.8 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.10, C:H.12, C:H.44

3 x 2AA: 5'-O-{[({[2-({[5-(DIMETHYLAMINO)NAPHTHALEN-1-YL]SULFONYL}AMINO)ETHYL]OXY}PHOSPHINATO)OXY]PHOSPHINATO}CYT(Non-covalent)

2AA.2: 23 residues within 4Å: Chain A: D.10, H.12, S.37, H.44, D.58, I.59, G.60, F.63, F.70, A.73, D.74, S.75, E.77, L.78 Chain B: A.102, P.105, K.106, M.107, L.108, A.133, T.134, T.135 Ligands: ZN.1 19 PLIP interactions: 12 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:F.63, A:F.70, A:A.73, A:L.78, A:L.78, B:A.133, B:T.135 Hydrogen bonds: A:H.36, A:D.58, A:G.60, B:A.102, B:M.107, B:L.108, B:T.135, B:T.135 Water bridges: A:S.37, A:S.37 Salt bridges: A:H.12, A:H.44 2AA.5: 23 residues within 4Å: Chain B: D.10, H.12, S.37, H.44, D.58, I.59, G.60, F.63, F.70, A.73, D.74, S.75, E.77, L.78 Chain C: A.102, P.105, K.106, M.107, L.108, A.133, T.134, T.135 Ligands: ZN.4 20 PLIP interactions: 12 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:F.63, B:F.70, B:A.73, B:L.78, B:L.78, C:A.133, C:T.135 Hydrogen bonds: B:H.36, B:D.58, B:G.60, C:A.102, C:M.107, C:L.108, C:T.134, C:T.135, C:T.135 Water bridges: B:S.37, B:S.37 Salt bridges: B:H.12, B:H.44 2AA.8: 23 residues within 4Å: Chain A: A.102, P.105, K.106, M.107, L.108, A.133, T.134, T.135 Chain C: D.10, H.12, S.37, H.44, D.58, I.59, G.60, F.63, F.70, A.73, D.74, S.75, E.77, L.78 Ligands: ZN.7 20 PLIP interactions: 8 interactions with chain A, 12 interactions with chain C Hydrophobic interactions: A:A.133, A:T.135, C:F.63, C:F.70, C:A.73, C:L.78, C:L.78 Hydrogen bonds: A:A.102, A:M.107, A:L.108, A:T.134, A:T.135, A:T.135, C:H.36, C:D.58, C:G.60 Water bridges: C:S.37, C:S.37 Salt bridges: C:H.12, C:H.44

3 x GPP: GERANYL DIPHOSPHATE(Non-covalent)

GPP.3: 19 residues within 4Å: Chain A: F.9, T.136, G.140, F.141, T.142, R.144, E.151 Chain B: F.9, I.101, G.140, F.141, R.144, E.151 Chain C: F.9, G.140, F.141, R.144 Ligands: GPP.6, GPP.9 17 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: B:F.9, B:I.101, A:F.9, A:T.136, A:F.141, C:F.9, C:F.141 Hydrogen bonds: B:F.141, A:F.141, C:G.140, C:F.141 Water bridges: B:R.144, B:E.146, A:R.144 Salt bridges: B:R.144, A:R.144, C:R.144 GPP.6: 19 residues within 4Å: Chain A: F.9, G.140, F.141, R.144 Chain B: F.9, T.136, G.140, F.141, T.142, R.144, E.151 Chain C: F.9, I.101, G.140, F.141, R.144, E.151 Ligands: GPP.3, GPP.9 17 PLIP interactions: 6 interactions with chain C, 5 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: C:F.9, C:I.101, A:F.9, A:F.141, B:F.9, B:T.136, B:F.141 Hydrogen bonds: C:F.141, A:G.140, A:F.141, B:F.141 Water bridges: C:R.144, C:E.146, B:R.144 Salt bridges: C:R.144, A:R.144, B:R.144 GPP.9: 19 residues within 4Å: Chain A: F.9, I.101, G.140, F.141, R.144, E.151 Chain B: F.9, G.140, F.141, R.144 Chain C: F.9, T.136, G.140, F.141, T.142, R.144, E.151 Ligands: GPP.3, GPP.6 17 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: A:F.9, A:I.101, B:F.9, B:F.141, C:F.9, C:T.136, C:F.141 Hydrogen bonds: A:F.141, B:G.140, B:F.141, C:F.141 Water bridges: A:R.144, A:E.146, C:R.144 Salt bridges: A:R.144, B:R.144, C:R.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crane, C.M. et al., Fluorescent Inhibitors for Ispf, an Enzyme in the Non-Mevalonate Pathway for Isoprenoid Biosynthesis and a Potential Target for Antimalarial Therapy. Angew.Chem.Int.Ed.Engl. (2006)

Release Date

2006-11-14

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