SMTL ID : 2amt.2 (1 other biounit)

Structure of 2C-Methyl-D-Erythritol 2,4-Clycodiphosphate Synthase complexed with a CDP derived fluorescent inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.8, H.10, H.42 Ligands: 1AA.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.8, A:H.10, A:H.42 ZN.4: 4 residues within 4Å: Chain B: D.8, H.10, H.42 Ligands: 1AA.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.8, B:D.8, B:H.10, B:H.42 ZN.7: 4 residues within 4Å: Chain C: D.8, H.10, H.42 Ligands: 1AA.2 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.8, C:D.8, C:H.10, C:H.42

3 x 1AA: 5'-O-[({[(2-{[(2-AMINOPHENYL)CARBONYL]OXY}ETHYL)OXY]PHOSPHINATO}OXY)PHOSPHINATO]CYTIDINE(Non-covalent)

1AA.2: 21 residues within 4Å: Chain A: A.100, A.102, P.103, K.104, M.105, L.106, A.131, T.132, T.133, E.135 Chain C: D.8, H.10, H.34, S.35, H.42, D.56, I.57, G.58, F.61, L.76 Ligands: ZN.7 19 PLIP interactions: 8 interactions with chain C, 11 interactions with chain A Hydrophobic interactions: C:I.57, C:F.61, C:L.76, A:A.131, A:T.133 Hydrogen bonds: C:D.56, C:G.58, C:D.63, A:A.100, A:A.102, A:K.104, A:M.105, A:L.106, A:T.133 Salt bridges: C:H.10, C:H.34 Water bridges: A:A.131, A:A.131 pi-Cation interactions: A:K.104 1AA.5: 19 residues within 4Å: Chain A: D.8, V.9, H.10, H.34, S.35, D.56, I.57, G.58, F.61 Chain B: A.100, P.103, K.104, M.105, L.106, A.131, T.132, T.133, E.135 Ligands: ZN.1 18 PLIP interactions: 9 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:A.131, B:T.133, A:I.57, A:F.61 Hydrogen bonds: B:A.100, B:K.104, B:M.105, B:L.106, B:T.133, B:T.133, A:D.8, A:H.34, A:H.34, A:D.56, A:G.58 Water bridges: B:A.131, A:D.56 Salt bridges: A:H.10 1AA.6: 22 residues within 4Å: Chain B: D.8, H.10, A.33, H.34, S.35, H.42, D.56, I.57, G.58, F.61, D.63, L.76 Chain C: A.100, P.103, K.104, M.105, L.106, A.131, T.132, T.133, E.135 Ligands: ZN.4 17 PLIP interactions: 8 interactions with chain C, 9 interactions with chain B Hydrophobic interactions: C:A.131, C:T.133, B:I.57, B:F.61, B:L.76 Hydrogen bonds: C:A.100, C:M.105, C:L.106, C:A.131, C:T.133, B:G.58, B:D.63 Water bridges: C:A.131, B:V.9, B:D.56 Salt bridges: B:H.10, B:H.42

1 x GPP: GERANYL DIPHOSPHATE(Non-covalent)

GPP.3: 13 residues within 4Å: Chain A: F.7, G.138, F.139, R.142, E.149 Chain B: F.7, G.138, F.139, R.142 Chain C: F.7, G.138, F.139, R.142 14 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: A:F.7, B:F.7, B:F.139, C:F.7 Hydrogen bonds: A:F.139, B:F.139, C:G.138, C:F.139 Salt bridges: A:R.142, B:R.142, C:R.142 Water bridges: B:R.142, B:E.144, C:R.142

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

2006-02-28

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

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

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