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

Crystal structure of enolase from Escherichia coli with bound 2-phosphoglycerate substrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-dimer

Ligands

2 x 2PG: 2-PHOSPHOGLYCERIC ACID(Non-covalent)

2PG.1: 18 residues within 4Å: Chain A: G.57, A.58, S.59, H.176, Q.184, E.185, E.226, D.263, E.307, D.334, L.357, K.359, H.387, R.388, S.389, K.410 Ligands: MG.2, MG.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:A.58, A:S.59, A:S.59, A:Q.184, A:E.226, A:S.389, A:S.389, A:K.410 Water bridges: A:N.169, A:Q.362, A:R.388 Salt bridges: A:H.176, A:K.359, A:K.359, A:R.388, A:K.410 2PG.10: 18 residues within 4Å: Chain B: G.57, A.58, S.59, H.176, Q.184, E.185, E.226, D.263, E.307, D.334, L.357, K.359, H.387, R.388, S.389, K.410 Ligands: MG.11, MG.12 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:A.58, B:S.59, B:S.59, B:Q.184, B:E.185, B:H.387, B:S.389, B:S.389, B:K.410 Water bridges: B:N.169, B:Q.362, B:R.388 Salt bridges: B:H.176, B:K.359, B:K.359, B:R.388, B:K.410

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.59, D.334, D.335 Ligands: 2PG.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.59, A:S.59, H2O.2, H2O.6 MG.3: 6 residues within 4Å: Chain A: D.263, A.265, E.307, D.308, D.334 Ligands: 2PG.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.263, A:D.263, A:D.308, H2O.6 MG.11: 3 residues within 4Å: Chain B: S.59, D.334 Ligands: 2PG.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.59, B:S.59, H2O.10, H2O.11 MG.12: 7 residues within 4Å: Chain B: D.263, A.265, E.307, D.308, D.334, D.335 Ligands: 2PG.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.263, B:D.308, B:D.334, H2O.11

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

SO4.4: 4 residues within 4Å: Chain A: K.197, E.198, R.201 Chain B: R.75 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Water bridges: A:K.197, A:R.201 Salt bridges: A:K.197, A:R.201, B:R.75 SO4.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.6: 4 residues within 4Å: Chain A: R.33, N.35, K.79 Chain B: H.208 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.35 Salt bridges: A:K.79, B:H.208 SO4.7: 3 residues within 4Å: Chain A: H.208 Chain B: R.33, N.35 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:H.208 Hydrogen bonds: B:N.35 SO4.8: 5 residues within 4Å: Chain A: G.218, M.219, N.220, P.231, N.232 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.220, A:N.232 SO4.9: 4 residues within 4Å: Chain A: R.75 Chain B: K.197, E.198, R.201 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Salt bridges: A:R.75, B:K.197, B:R.201 Hydrogen bonds: B:K.197 Water bridges: B:E.198 SO4.13: 5 residues within 4Å: Chain B: K.137, D.394, A.395, T.396, D.399 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.395, B:T.396 Salt bridges: B:K.137

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 3 residues within 4Å: Chain A: R.15 Chain B: G.14, R.15 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.15, A:R.15, A:R.15 Water bridges: B:G.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krucinska, J. et al., Structural and Functional Studies of Bacterial Enolase, a Potential Target against Gram-Negative Pathogens. Biochemistry (2019)

Release Date

2018-10-31

Peptides

Enolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Enolase

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