SMTL ID : 6d3q.3 (2 other biounits)

Crystal structure of Escherichia coli enolase complexed with a natural inhibitor SF2312.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 Å

Oligo State

homo-dimer

Ligands

2 x 4NG: [(3S,5S)-1,5-dihydroxy-2-oxopyrrolidin-3-yl]phosphonic acid(Non-covalent)

4NG.1: 17 residues within 4Å: Chain A: G.47, A.48, S.49, Q.174, E.175, E.216, D.253, E.297, D.324, L.347, K.349, H.377, R.378, S.379, K.400 Ligands: MG.2, MG.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:A.48, A:S.49, A:Q.174, A:D.324, A:K.349, A:K.349, A:H.377, A:R.378, A:S.379, A:K.400 Water bridges: A:N.159 4NG.7: 17 residues within 4Å: Chain B: G.47, A.48, S.49, Q.174, E.175, E.216, D.253, E.297, D.324, L.347, K.349, H.377, R.378, S.379, K.400 Ligands: MG.8, MG.9 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:A.48, B:S.49, B:Q.174, B:E.216, B:D.253, B:D.253, B:K.349, B:R.378, B:S.379, B:S.379, B:K.400 Water bridges: B:N.159, B:Q.352

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.253, E.297, D.324, K.349, K.400 Ligands: 4NG.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.253, A:E.297, A:D.324, H2O.2 MG.3: 3 residues within 4Å: Chain A: S.49, D.324 Ligands: 4NG.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.49, A:S.49, H2O.1, H2O.2 MG.8: 6 residues within 4Å: Chain B: D.253, E.297, D.324, K.349, K.400 Ligands: 4NG.7 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.253, B:E.297, B:D.324, H2O.6 MG.9: 3 residues within 4Å: Chain B: S.49, D.324 Ligands: 4NG.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.49, B:S.49, H2O.5, H2O.6

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: I.102, T.107, E.108, K.110, K.332, I.353, E.358 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.107, A:K.332, A:K.332, A:E.358 Water bridges: A:K.110, A:K.110, A:N.330 GOL.10: 7 residues within 4Å: Chain B: I.102, T.107, E.108, K.110, K.332, I.353, E.358 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.110, B:K.332 Water bridges: B:K.110, B:K.110

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

SO4.5: 4 residues within 4Å: Chain A: K.187, E.188, R.191 Chain B: R.65 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.187, A:R.191, B:R.65 SO4.6: 4 residues within 4Å: Chain A: T.107, E.108, N.109, S.111 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.107, A:E.108, A:N.109, A:S.111, A:S.111 SO4.11: 2 residues within 4Å: Chain A: R.5 Chain B: R.5 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Salt bridges: A:R.5, B:R.5 Water bridges: B:R.5, B:G.6, B:G.6 SO4.12: 4 residues within 4Å: Chain A: R.65 Chain B: K.187, E.188, R.191 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.65, B:K.187, B:R.191 SO4.13: 4 residues within 4Å: Chain B: T.107, E.108, N.109, S.111 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.107, B:E.108, B:N.109, B:N.109, B:S.111, B:S.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krucinska, J. et al., Functional and structural basis of E. coli enolase inhibition by SF2312: a mimic of the carbanion intermediate. Sci Rep (2019)

Release Date

2019-11-27

Peptides

Enolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

Enolase

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