SMTL ID : 7m66.1 (1 other biounit)

Targeting Enterococcus faecalis HMG-CoA reductase with a novel non-statin inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: A.180, M.181, G.182, A.183, N.184, I.185, G.324, G.325 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:M.181, A:G.182, A:A.183, A:N.184, A:N.184, A:G.325

3 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 8 residues within 4Å: Chain A: L.69, H.70, S.94, K.98 Chain B: Y.15, Q.16, N.56 Ligands: MES.10 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.94 Water bridges: A:H.70 Salt bridges: A:H.70 pi-Cation interactions: B:Y.15 MES.9: 10 residues within 4Å: Chain A: E.86, P.87 Chain B: A.180, M.181, G.182, A.183, N.184, I.185, G.324, G.325 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:M.181, B:G.182, B:A.183, B:N.184, B:G.325 MES.10: 9 residues within 4Å: Chain A: L.69, H.70, L.79 Chain B: R.13, F.14, S.25, L.26, E.29 Ligands: MES.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.14 Water bridges: B:R.13

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

PEG.3: 11 residues within 4Å: Chain A: S.252, K.293, E.294, Q.298, G.299, L.300, T.301, S.302, E.313, I.314, S.315 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.300 Water bridges: A:S.315 PEG.4: 8 residues within 4Å: Chain A: Y.214, V.292, K.293, E.294, G.295 Chain B: G.295, R.296, Y.297 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.294, A:G.295, B:G.295 PEG.5: 9 residues within 4Å: Chain A: E.86, S.88, V.89, A.92, G.264, N.267, Q.359, A.362, A.363 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.267, A:Q.359, A:A.363

5 x CA: CALCIUM ION(Non-covalent)

CA.6: 2 residues within 4Å: Chain A: T.343, E.347 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.343, A:E.347, A:E.347, H2O.4, H2O.5 CA.7: 5 residues within 4Å: Chain A: D.338, L.339, A.341 Chain B: Q.31, I.32 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:Q.31, A:D.338, A:D.338, H2O.6, H2O.12 CA.8: 4 residues within 4Å: Chain A: E.135, D.158, L.159, Q.160 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.158, A:L.159, H2O.1, H2O.4, H2O.6 CA.14: 5 residues within 4Å: Chain A: Q.31, I.32 Chain B: D.338, L.339, A.341 5 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:Q.31, B:D.338, H2O.5, H2O.6, H2O.11 CA.15: 3 residues within 4Å: Chain B: I.128, D.129, Q.132 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.129, H2O.7, H2O.12, H2O.12

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

EDO.11: 6 residues within 4Å: Chain A: P.255, Y.297 Chain B: Y.214, A.289, F.290, V.292 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.214 EDO.12: 7 residues within 4Å: Chain B: V.73, D.74, T.76, Y.78, T.105, E.347, R.350 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.74, B:E.347, B:R.350, B:R.350 EDO.13: 3 residues within 4Å: Chain B: R.162, A.163, F.164 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.163, B:A.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bose, S. et al., Targeting Enterococcus faecalis HMG-CoA reductase with a non-statin inhibitor. Commun Biol (2023)

Release Date

2022-09-28

Peptides

Hydroxymethylglutaryl-CoA reductase, degradative: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hydroxymethylglutaryl-CoA reductase, degradative

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