SMTL ID : 6v3m.1

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in compomplex with ligand HGN-0961 (BSI110840)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-trimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.31, H.33, H.65 Ligands: QOG.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.31, A:H.33, A:H.65 ZN.7: 4 residues within 4Å: Chain B: D.31, H.33, H.65 Ligands: QOG.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.31, B:D.31, B:H.33, B:H.65 ZN.12: 4 residues within 4Å: Chain C: D.31, H.33, H.65 Ligands: QOG.13 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.31, C:H.33, C:H.65

3 x QOG: 5-{[(propan-2-yl)carbamoyl]amino}-1,3,4-thiadiazole-2-sulfonamide(Non-covalent)

QOG.2: 15 residues within 4Å: Chain A: D.31, H.33, H.57, S.58, H.65, I.80, G.81, F.84, S.85, D.86, F.91, A.94, L.99 Chain B: K.155 Ligands: ZN.1 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.99 Hydrogen bonds: A:S.58, A:F.84, A:F.84, A:D.86, B:K.155 Water bridges: A:S.58, B:T.156 pi-Stacking: A:H.65 QOG.8: 12 residues within 4Å: Chain B: D.31, H.33, S.58, H.65, I.80, G.81, F.84, S.85, F.91, L.99 Chain C: K.155 Ligands: ZN.7 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.91 Hydrogen bonds: B:S.58, B:F.84, B:F.84, C:K.155 pi-Stacking: B:H.65 Water bridges: C:A.154, C:T.156 QOG.13: 13 residues within 4Å: Chain A: K.155, E.158 Chain C: D.31, H.33, S.58, H.65, I.80, G.81, F.84, S.85, F.91, L.99 Ligands: ZN.12 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:K.155, A:K.155, C:F.84, C:F.84 Water bridges: A:T.156 Hydrophobic interactions: C:F.91

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

DMS.3: 8 residues within 4Å: Chain A: A.123, Q.124, A.125, P.126, K.127, L.128, K.155, T.156 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:L.128 Water bridges: C:R.82 DMS.4: 3 residues within 4Å: Chain A: D.144, L.145, P.146 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.144 DMS.9: 8 residues within 4Å: Chain B: A.123, Q.124, P.126, K.127, L.128, A.154, K.155, T.156 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.128, B:A.129 DMS.10: 3 residues within 4Å: Chain B: D.144, L.145, P.146 No protein-ligand interaction detected (PLIP) DMS.14: 8 residues within 4Å: Chain C: A.123, Q.124, A.125, P.126, K.127, L.128, K.155, T.156 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.128

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

EDO.5: 5 residues within 4Å: Chain A: A.113, I.114, L.143, D.144, L.145 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.114, A:L.143 EDO.11: 5 residues within 4Å: Chain B: A.113, I.114, L.143, D.144, L.145 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.114, B:D.144 EDO.15: 3 residues within 4Å: Chain C: D.144, L.145, P.146 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.144

1 x MLT: D-MALATE(Non-covalent)

MLT.6: 8 residues within 4Å: Chain A: G.161, Y.162, R.165 Chain B: G.161, Y.162 Chain C: G.161, Y.162, R.165 11 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A, 3 interactions with chain C Hydrogen bonds: B:Y.162, A:Y.162, A:R.165, C:Y.162 Water bridges: B:R.165, B:R.165, A:G.161, C:N.157 Hydrophobic interactions: A:Y.162 Salt bridges: A:R.165, C:R.165

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 compomplex with ligand HGN-0961 (BSI110840). to be published

Release Date

2020-12-09

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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