SMTL ID : 6nmo.1

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand SR-4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.11, H.13, H.45 Ligands: MLI.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.11, A:H.13, A:H.45, H2O.1, H2O.1 ZN.5: 3 residues within 4Å: Chain B: D.11, H.13, H.45 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.11, B:D.11, B:H.13, B:H.45, H2O.18 ZN.9: 4 residues within 4Å: Chain C: D.11, H.13, H.45 Ligands: QMS.10 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.11, C:H.13, C:H.45, H2O.15

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 8 residues within 4Å: Chain A: A.103, Q.104, A.105, P.106, K.107, L.108, K.135, T.136 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.108, A:A.109

3 x MLI: MALONATE ION(Non-functional Binders)

MLI.3: 8 residues within 4Å: Chain A: H.13, G.36, H.37, S.38, H.45, I.60, D.66 Ligands: ZN.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:D.66 Hydrogen bonds: A:H.37, A:S.38, A:S.38 Water bridges: A:S.38 Salt bridges: A:H.13, A:H.13, A:H.45, A:H.45 MLI.4: 9 residues within 4Å: Chain A: G.141, Y.142, R.145 Chain B: G.141, Y.142, R.145 Chain C: G.141, Y.142, R.145 15 PLIP interactions: 5 interactions with chain A, 6 interactions with chain C, 4 interactions with chain B Hydrogen bonds: A:Y.142, C:Y.142, B:Y.142 Water bridges: A:Y.142, A:Y.142, A:R.145, C:R.145, C:R.145, C:R.145, B:R.145, B:R.145 Salt bridges: A:R.145, C:R.145, B:R.145 Hydrophobic interactions: C:Y.142 MLI.8: 8 residues within 4Å: Chain A: Y.10, Y.142, L.143, E.150 Chain B: E.150, Q.152 Chain C: Y.10, Y.142 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:Q.152, C:Y.10, C:Y.142 Water bridges: B:N.137, A:N.137, A:E.150

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 4 residues within 4Å: Chain B: K.107, L.108, A.109, A.134 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.106, B:L.108, B:A.109 EDO.7: 3 residues within 4Å: Chain B: G.61, R.62 Chain C: A.109 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.61 EDO.11: 4 residues within 4Å: Chain C: K.107, L.108, A.109, A.134 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.108, C:A.109

1 x QMS: N-(QUINOLIN-8-YL)METHANESULFONAMIDE(Non-covalent)

QMS.10: 11 residues within 4Å: Chain A: K.135, E.138 Chain C: D.11, H.13, L.35, G.36, H.37, A.40, H.45, I.60 Ligands: ZN.9 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.60, C:I.60 Hydrogen bonds: C:H.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand SR-4. To be Published

Release Date

2020-01-15

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