SMTL ID : 8qc7.2 (1 other biounit)

New monoclinic EcIspE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

monomer

Ligands

1 x CDM: 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL(Non-covalent)

CDM.1: 21 residues within 4Å: Chain A: K.10, N.12, L.15, G.24, Y.25, H.26, L.28, F.32, S.108, G.139, A.140, D.141, V.156, T.181, P.182, F.185, K.186, G.239, T.240 Ligands: ADP.2, MG.3 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:Y.25, A:A.140, A:F.185, A:T.240 Hydrogen bonds: A:K.10, A:K.10, A:N.12, A:Y.25, A:Y.25, A:H.26, A:H.26, A:H.26, A:A.140, A:D.141, A:D.141, A:V.156, A:K.186 Water bridges: A:Q.20, A:S.108, A:T.181 pi-Stacking: A:F.185

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

ADP.2: 21 residues within 4Å: Chain A: V.57, G.59, V.60, D.64, N.65, L.66, I.67, K.96, V.100, G.101, G.102, G.103, L.104, G.105, G.106, G.107, S.108, N.110, T.181 Ligands: CDM.1, MG.3 18 PLIP interactions: 18 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.103, A:G.105, A:G.106, A:G.107, A:S.108, A:T.181, A:T.181 Water bridges: A:G.59, A:L.104, A:L.104, A:T.240

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: S.108 Ligands: CDM.1, ADP.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.108, H2O.1, H2O.1

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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