SMTL ID : 6npf.2 (2 other biounits)

Structure of E.coli enolase in complex with an analog of the natural product SF-2312 metabolite.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: K.197, E.198, R.201 Chain B: R.75 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.201, B:R.75 SO4.4: 3 residues within 4Å: Chain A: K.446, G.447, Q.448 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.447 Salt bridges: A:K.446 SO4.7: 4 residues within 4Å: Chain A: R.75 Chain B: K.197, E.198, R.201 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:K.197, B:R.201, A:R.75 SO4.8: 3 residues within 4Å: Chain A: R.15 Chain B: G.14, R.15 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.15, B:R.15 Water bridges: B:R.15 Salt bridges: B:R.15 SO4.11: 7 residues within 4Å: Chain A: R.428 Chain B: E.39, M.51, A.52, A.53, E.393, D.394 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.39, B:E.39, B:D.394 Salt bridges: B:K.137

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: D.263, E.307, D.308, D.334, L.357, K.359 Ligands: TLA.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.263, A:E.307, A:D.334, H2O.1 MG.9: 6 residues within 4Å: Chain B: D.263, E.307, D.334, K.359, K.410 Ligands: KVM.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.263, B:E.307, B:D.334, H2O.3

1 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.3: 15 residues within 4Å: Chain A: G.57, A.58, S.59, H.176, Q.184, E.185, D.263, E.307, D.334, L.357, K.359, R.388, S.389, K.410 Ligands: MG.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:A.58, A:S.59, A:Q.184, A:E.185, A:E.185, A:D.263, A:K.359, A:K.359, A:R.388, A:S.389 Water bridges: A:Q.362, A:K.410 Salt bridges: A:K.359, A:K.359, A:R.388, A:K.410

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 1 residues within 4Å: Chain A: M.13 No protein-ligand interaction detected (PLIP) GOL.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x KVM: [(3S)-1-hydroxy-2,5-dioxopyrrolidin-3-yl]phosphonic acid(Non-covalent)

KVM.6: 17 residues within 4Å: Chain B: G.57, A.58, S.59, Q.184, E.185, E.226, D.263, E.307, D.334, L.357, K.359, S.386, H.387, R.388, S.389, K.410 Ligands: MG.9 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:A.58, B:S.59, B:Q.184, B:D.263, B:K.359, B:S.386, B:R.388, B:R.388, B:R.388, B:S.389, B:K.410

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
C

B
D

Enolase

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