SMTL ID : 8qcc.2 (1 other biounit)

E.coli IspE in complex with a ligand (1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 21 residues within 4Å: Chain A: V.57, V.60, D.64, N.65, L.66, I.67, K.96, P.99, V.100, G.101, G.102, G.103, L.104, G.105, G.106, G.107, S.108, N.110, D.141, T.181 Ligands: MG.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.65, A:N.65, A:L.66, A:K.96, A:G.101, A:G.102, A:G.103, A:G.105, A:G.106, A:G.107, A:S.108, A:D.141, A:T.181 Water bridges: A:G.101, A:L.104, A:T.240

1 x UKO: ~{N}-[3-[4-azanyl-2-oxidanylidene-1-[(2~{R})-thiolan-2-yl]pyrimidin-5-yl]prop-2-ynyl]cyclopropanesulfonamide(Non-covalent)

UKO.2: 17 residues within 4Å: Chain A: K.10, N.12, L.15, G.24, Y.25, H.26, T.27, L.28, F.32, A.140, D.141, V.156, G.157, T.181, F.185, G.239, T.240 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.15, A:Y.25, A:Y.25, A:A.140, A:F.185 Hydrogen bonds: A:K.10, A:N.12, A:H.26, A:H.26, A:H.26, A:D.141 pi-Stacking: A:F.185

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: S.108, D.141 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.108 MG.4: 3 residues within 4Å: Chain A: P.8, Y.37, G.38 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain A: P.143, R.147, E.158, L.160 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.158, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hamid, R. et al., IspE kinase as an anti-infective target: Role of a hydrophobic pocket in inhibitor binding. Structure (2024)

Release Date

2024-09-11

Peptides

4-diphosphocytidyl-2-C-methyl-D-erythritol kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

4-diphosphocytidyl-2-C-methyl-D-erythritol kinase

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