SMTL ID : 6mwi.1

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0456

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: D.14, H.16, H.48 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.14, A:H.16, A:H.48, H2O.6, H2O.11 ZN.4: 4 residues within 4Å: Chain B: D.14, H.16, H.48 Ligands: EZL.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.14, B:D.14, B:H.16, B:H.48 ZN.7: 3 residues within 4Å: Chain C: D.14, H.16, H.48 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.14, C:H.16, C:H.48, H2O.5, H2O.14, H2O.17

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

DMS.2: 8 residues within 4Å: Chain A: A.106, Q.107, A.108, P.109, K.110, L.111, K.138, T.139 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Water bridges: C:R.65 Hydrogen bonds: A:L.111 DMS.8: 8 residues within 4Å: Chain C: A.106, Q.107, A.108, P.109, K.110, L.111, K.138, T.139 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.111 Water bridges: C:A.112

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 4 residues within 4Å: Chain A: A.96, I.97, L.126, D.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.97, A:D.127

1 x EZL: 6-ethoxy-1,3-benzothiazole-2-sulfonamide(Non-covalent)

EZL.5: 10 residues within 4Å: Chain B: D.14, H.16, H.48, I.63, F.67, S.68, D.69, F.74 Chain C: K.138 Ligands: ZN.4 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:F.74 Hydrogen bonds: B:D.14, C:K.138 pi-Stacking: B:H.48 Water bridges: C:T.139, C:E.141, C:E.141

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 10 residues within 4Å: Chain B: A.106, Q.107, A.108, P.109, K.110, L.111, A.112, A.137, K.138, T.139 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.107, B:L.111, B:A.112

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 HGN-0456. To Be Published

Release Date

2019-11-06

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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