SMTL ID : 5boe.1

Crystal structure of Staphylococcus aureus enolase in complex with PEP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-octamer

Ligands

8 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.1: 14 residues within 4Å: Chain A: G.40, A.41, S.42, E.166, D.244, E.291, D.318, L.341, K.343, H.371, R.372, S.373, K.394 Ligands: MG.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.41, A:S.373, A:S.373 Salt bridges: A:K.343, A:K.343, A:R.372, A:K.394 PEP.4: 11 residues within 4Å: Chain B: E.166, D.244, E.291, D.318, L.341, K.343, H.371, R.372, S.373, K.394 Ligands: MG.5 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.166, B:D.244, B:S.373 Water bridges: B:K.394 Salt bridges: B:K.343, B:K.343, B:R.372, B:K.394 PEP.8: 14 residues within 4Å: Chain C: G.40, A.41, S.42, E.166, D.244, E.291, D.318, L.341, K.343, H.371, R.372, S.373, K.394 Ligands: MG.9 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:A.41, C:S.373, C:S.373 Salt bridges: C:K.343, C:K.343, C:R.372, C:K.394 PEP.11: 11 residues within 4Å: Chain D: E.166, D.244, E.291, D.318, L.341, K.343, H.371, R.372, S.373, K.394 Ligands: MG.12 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:E.166, D:D.244, D:S.373 Water bridges: D:K.394 Salt bridges: D:K.343, D:K.343, D:R.372, D:K.394 PEP.15: 14 residues within 4Å: Chain E: G.40, A.41, S.42, E.166, D.244, E.291, D.318, L.341, K.343, H.371, R.372, S.373, K.394 Ligands: MG.16 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:A.41, E:S.373, E:S.373 Salt bridges: E:K.343, E:K.343, E:R.372, E:K.394 PEP.18: 11 residues within 4Å: Chain F: E.166, D.244, E.291, D.318, L.341, K.343, H.371, R.372, S.373, K.394 Ligands: MG.19 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:E.166, F:D.244, F:S.373 Water bridges: F:K.394 Salt bridges: F:K.343, F:K.343, F:R.372, F:K.394 PEP.22: 14 residues within 4Å: Chain G: G.40, A.41, S.42, E.166, D.244, E.291, D.318, L.341, K.343, H.371, R.372, S.373, K.394 Ligands: MG.23 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:A.41, G:S.373, G:S.373 Salt bridges: G:K.343, G:K.343, G:R.372, G:K.394 PEP.25: 11 residues within 4Å: Chain H: E.166, D.244, E.291, D.318, L.341, K.343, H.371, R.372, S.373, K.394 Ligands: MG.26 8 PLIP interactions: 8 interactions with chain H Hydrogen bonds: H:E.166, H:D.244, H:S.373 Water bridges: H:K.394 Salt bridges: H:K.343, H:K.343, H:R.372, H:K.394

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.244, E.291, D.318 Ligands: PEP.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.244, A:E.291, A:D.318, H2O.4, H2O.4 MG.5: 4 residues within 4Å: Chain B: D.244, E.291, D.318 Ligands: PEP.4 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.244, B:E.291, B:D.318, H2O.15, H2O.18 MG.9: 4 residues within 4Å: Chain C: D.244, E.291, D.318 Ligands: PEP.8 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.244, C:E.291, C:D.318, H2O.29, H2O.29 MG.12: 4 residues within 4Å: Chain D: D.244, E.291, D.318 Ligands: PEP.11 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.244, D:E.291, D:D.318, H2O.41, H2O.44 MG.16: 4 residues within 4Å: Chain E: D.244, E.291, D.318 Ligands: PEP.15 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.244, E:E.291, E:D.318, H2O.55, H2O.55 MG.19: 4 residues within 4Å: Chain F: D.244, E.291, D.318 Ligands: PEP.18 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.244, F:E.291, F:D.318, H2O.66, H2O.69 MG.23: 4 residues within 4Å: Chain G: D.244, E.291, D.318 Ligands: PEP.22 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.244, G:E.291, G:D.318, H2O.80, H2O.80 MG.26: 4 residues within 4Å: Chain H: D.244, E.291, D.318 Ligands: PEP.25 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.244, H:E.291, H:D.318, H2O.92, H2O.95

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: P.131, Y.133, Q.409, R.412, I.413, E.416 Chain B: E.24, R.34 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.34, A:Q.409, A:Q.409 Water bridges: B:R.10, B:E.24, A:R.412 GOL.6: 8 residues within 4Å: Chain A: E.24, R.34 Chain B: P.131, Y.133, Q.409, R.412, I.413, E.416 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.34, B:Q.409 Water bridges: A:R.10, A:E.24, B:Q.409, B:R.412 GOL.7: 7 residues within 4Å: Chain B: K.134, E.416, L.417, F.418, E.419 Chain G: D.88, S.91 10 PLIP interactions: 4 interactions with chain G, 6 interactions with chain B Hydrogen bonds: G:S.91, G:S.91, B:K.134, B:E.419 Water bridges: G:D.88, G:D.88, B:K.134, B:K.134, B:K.134, B:K.134 GOL.10: 8 residues within 4Å: Chain C: P.131, Y.133, Q.409, R.412, I.413, E.416 Chain D: E.24, R.34 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.409, C:Q.409, D:R.34 Water bridges: C:R.412, D:R.10, D:E.24 GOL.13: 8 residues within 4Å: Chain C: E.24, R.34 Chain D: P.131, Y.133, Q.409, R.412, I.413, E.416 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Q.409, C:R.34 Water bridges: D:Q.409, D:R.412, C:R.10, C:E.24 GOL.14: 7 residues within 4Å: Chain D: K.134, E.416, L.417, F.418, E.419 Chain E: D.88, S.91 10 PLIP interactions: 6 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:K.134, D:E.419, E:S.91, E:S.91 Water bridges: D:K.134, D:K.134, D:K.134, D:K.134, E:D.88, E:D.88 GOL.17: 8 residues within 4Å: Chain E: P.131, Y.133, Q.409, R.412, I.413, E.416 Chain F: E.24, R.34 6 PLIP interactions: 3 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:R.34, E:Q.409, E:Q.409 Water bridges: F:R.10, F:E.24, E:R.412 GOL.20: 8 residues within 4Å: Chain E: E.24, R.34 Chain F: P.131, Y.133, Q.409, R.412, I.413, E.416 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:R.34, F:Q.409 Water bridges: E:R.10, E:E.24, F:Q.409, F:R.412 GOL.21: 7 residues within 4Å: Chain A: D.88, S.91 Chain F: K.134, E.416, L.417, F.418, E.419 10 PLIP interactions: 6 interactions with chain F, 4 interactions with chain A Hydrogen bonds: F:K.134, F:E.419, A:S.91, A:S.91 Water bridges: F:K.134, F:K.134, F:K.134, F:K.134, A:D.88, A:D.88 GOL.24: 8 residues within 4Å: Chain G: P.131, Y.133, Q.409, R.412, I.413, E.416 Chain H: E.24, R.34 6 PLIP interactions: 3 interactions with chain H, 3 interactions with chain G Hydrogen bonds: H:R.34, G:Q.409, G:Q.409 Water bridges: H:R.10, H:E.24, G:R.412 GOL.27: 8 residues within 4Å: Chain G: E.24, R.34 Chain H: P.131, Y.133, Q.409, R.412, I.413, E.416 6 PLIP interactions: 3 interactions with chain G, 3 interactions with chain H Hydrogen bonds: G:R.34, H:Q.409 Water bridges: G:R.10, G:E.24, H:Q.409, H:R.412 GOL.28: 7 residues within 4Å: Chain C: D.88, S.91 Chain H: K.134, E.416, L.417, F.418, E.419 10 PLIP interactions: 6 interactions with chain H, 4 interactions with chain C Hydrogen bonds: H:K.134, H:E.419, C:S.91, C:S.91 Water bridges: H:K.134, H:K.134, H:K.134, H:K.134, C:D.88, C:D.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, Y. et al., Octameric structure of Staphylococcus aureus enolase in complex with phosphoenolpyruvate. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-12-09

Peptides

Enolase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Enolase

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