SMTL ID : 8xkf.1 (1 other biounit)

Crystal structure of Helicobacter pylori IspDF with substrate CTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

EDO.2: 7 residues within 4Å: Chain A: S.321, P.324, K.325, I.326, A.352, T.353, T.354 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.324, A:I.326 EDO.3: 4 residues within 4Å: Chain A: T.353, T.354, E.356 Chain B: D.284 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.353, A:T.354, B:D.284 EDO.4: 5 residues within 4Å: Chain A: D.105, R.108, I.156, K.177, D.178 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.85, A:R.108, A:I.156 EDO.8: 4 residues within 4Å: Chain B: H.263, G.279, F.282, D.284 No protein-ligand interaction detected (PLIP)

3 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.5: 18 residues within 4Å: Chain A: L.16, A.17, A.18, G.19, E.20, S.21, R.22, R.23, K.30, G.82, A.83, S.84, R.85, S.88, D.105, V.106, A.107, K.202 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:A.17, A:A.18, A:G.19, A:E.20, A:S.21, A:R.22, A:R.23, A:R.23, A:G.82, A:S.88, A:V.106, A:A.107 Water bridges: A:K.30, A:Q.31 Salt bridges: A:R.23, A:K.30, A:K.30, A:K.30, A:K.202 CTP.9: 17 residues within 4Å: Chain B: L.16, A.17, A.18, G.19, E.20, S.21, R.22, R.23, K.30, G.82, A.83, S.84, R.85, S.88, D.105, V.106, A.107 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:A.17, B:A.18, B:G.19, B:E.20, B:S.21, B:R.22, B:R.23, B:R.23, B:G.82, B:S.88, B:D.105, B:V.106, B:A.107 Salt bridges: B:R.23, B:K.30, B:K.30, B:K.30 CTP.12: 18 residues within 4Å: Chain C: L.16, A.17, A.18, G.19, E.20, S.21, R.22, R.23, K.30, G.82, A.83, S.84, R.85, S.88, D.105, V.106, A.107, K.202 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:A.17, C:A.18, C:G.19, C:G.19, C:E.20, C:S.21, C:R.22, C:R.23, C:R.23, C:G.82, C:S.88, C:V.106, C:A.107 Salt bridges: C:R.23, C:K.30, C:K.30, C:K.30, C:K.202

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: K.220, D.221, T.222 Chain C: T.222, F.313, R.376 Ligands: GOL.14 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:T.222, C:R.376, A:D.221, A:D.221, A:T.222, A:T.222 Water bridges: A:K.220, A:D.221 GOL.14: 7 residues within 4Å: Chain A: K.220, T.222 Chain B: K.220, T.222 Chain C: K.220, T.222 Ligands: GOL.6 10 PLIP interactions: 6 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:K.220, B:T.222, C:K.220, C:T.222, A:K.220, A:T.222 Water bridges: B:T.222, B:T.222, B:T.222, B:T.222 GOL.15: 7 residues within 4Å: Chain B: S.346, Q.347 Chain C: H.37, F.223, K.274, F.310, Y.377 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.274, C:K.274, C:Y.377 Water bridges: C:Y.68

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain A: D.229, H.231, H.263 Ligands: CDP.13 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.231, A:H.263

1 x C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)

C5P.10: 14 residues within 4Å: Chain B: S.321, P.324, K.325, I.326, T.327, K.330, A.352, T.353, T.354, E.356 Chain C: D.277, I.278, G.279, E.280 14 PLIP interactions: 2 interactions with chain C, 12 interactions with chain B Hydrogen bonds: C:D.277, C:G.279, B:S.321, B:K.325, B:I.326, B:T.327, B:T.327, B:K.330, B:T.353, B:T.354, B:T.354, B:E.356, B:E.356 Hydrophobic interactions: B:T.354

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.11: 6 residues within 4Å: Chain A: G.359, F.360 Chain B: G.359, F.360 Chain C: G.359, F.360 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:F.360, A:F.360, B:F.360

1 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.13: 20 residues within 4Å: Chain A: D.229, H.231, H.263, D.277, I.278, G.279, E.280, D.284 Chain C: S.321, E.322, P.324, K.325, I.326, T.327, K.330, A.352, T.353, T.354, E.356 Ligands: ZN.7 16 PLIP interactions: 6 interactions with chain A, 10 interactions with chain C Hydrogen bonds: A:D.277, A:G.279, C:S.321, C:I.326, C:T.327, C:T.327, C:K.330, C:T.353, C:T.354, C:E.356 Water bridges: A:I.278, A:D.284 Salt bridges: A:H.231, A:H.263 Hydrophobic interactions: C:T.354 pi-Cation interactions: C:K.325

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, X. et al., Two natural compounds as potential inhibitors against the Helicobacter pylori and Acinetobacter baumannii IspD enzymes. Int J Antimicrob Agents (2024)

Release Date

2024-04-10

Peptides

Bifunctional enzyme IspD/IspF: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Bifunctional enzyme IspD/IspF

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