SMTL ID : 2amt.1 (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: 5 residues within 4Å: Chain A: D.8, H.10, H.34, H.42 Ligands: 1AA.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.8, 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.5: 4 residues within 4Å: Chain C: D.8, H.10, H.42 Ligands: 1AA.7 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: 22 residues within 4Å: Chain A: D.8, H.10, H.34, S.35, D.56, I.57, G.58, F.61, P.62, D.63, F.68, L.76 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 A, 9 interactions with chain B Hydrophobic interactions: A:L.76, B:T.133 Hydrogen bonds: A:V.9, A:D.56, A:G.58, A:P.62, B:A.100, B:M.105, B:L.106, B:T.132, B:T.133, B:T.133, B:E.135 Water bridges: A:D.56, B:A.131 Salt bridges: A:H.10, A:H.34, A:H.34 1AA.6: 21 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, L.76 Chain C: A.100, Q.101, P.103, K.104, M.105, L.106, A.131, T.132, T.133 Ligands: ZN.4 18 PLIP interactions: 7 interactions with chain C, 11 interactions with chain B Hydrophobic interactions: C:A.131, C:T.133, B:I.57, B:I.57, B:F.61, B:F.61, B:L.76 Hydrogen bonds: C:A.100, C:M.105, C:L.106, C:T.133, C:T.133, B:D.56, B:G.58, B:F.61 Salt bridges: B:H.10, B:H.42 pi-Stacking: B:H.42 1AA.7: 21 residues within 4Å: Chain A: A.100, P.103, K.104, M.105, L.106, A.131, T.132, T.133, E.135 Chain C: D.8, H.10, A.33, H.34, S.35, H.42, D.56, I.57, G.58, K.59, D.63 Ligands: ZN.5 18 PLIP interactions: 10 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: A:A.131, A:T.133 Hydrogen bonds: A:A.100, A:M.105, A:L.106, A:T.132, A:T.133, A:T.133, C:H.34, C:D.56, C:I.57, C:K.59, C:D.63 Water bridges: A:A.131, A:A.131, C:V.9 Salt bridges: C:H.10, C:H.42

1 x GPP: GERANYL DIPHOSPHATE(Non-covalent)

GPP.3: 15 residues within 4Å: Chain A: F.7, G.138, F.139, T.140, R.142 Chain B: F.7, I.99, G.138, F.139, R.142 Chain C: F.7, G.138, F.139, R.142, E.149 14 PLIP interactions: 4 interactions with chain C, 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: C:F.7, C:F.139, A:F.7, A:F.139, A:T.140, B:I.99 Hydrogen bonds: C:F.139, A:F.139, B:F.139 Salt bridges: C:R.142, A:R.142, B:R.142 Water bridges: A:R.142, B: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
A

B
B

C
C

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

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