SMTL ID : 5j04.1

Crystal structure of Enolase from Synechococcus elongatus, complex with phosphoenolpyruvate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-octamer

Ligands

8 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.1: 14 residues within 4Å: Chain A: G.41, A.42, E.164, D.242, E.283, D.310, L.333, K.335, H.363, R.364, S.365, K.386 Ligands: CA.2, CA.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.242, A:S.365 Water bridges: A:E.164, A:D.310, A:D.310, A:K.335, A:K.335, A:H.363 Salt bridges: A:K.335, A:K.335, A:R.364, A:K.386 PEP.7: 12 residues within 4Å: Chain B: G.41, A.42, E.164, D.242, D.310, K.335, H.363, R.364, S.365, K.386 Ligands: CA.8, CA.9 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:A.42, B:S.365, B:S.365 Water bridges: B:E.164, B:D.310, B:K.335 Salt bridges: B:K.335, B:K.335, B:R.364, B:K.386 PEP.12: 14 residues within 4Å: Chain C: G.41, A.42, E.164, D.242, E.283, D.310, L.333, K.335, H.363, R.364, S.365, K.386 Ligands: CA.13, CA.14 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:D.242, C:S.365 Water bridges: C:E.164, C:D.310, C:D.310, C:K.335, C:K.335, C:H.363 Salt bridges: C:K.335, C:K.335, C:R.364, C:K.386 PEP.18: 12 residues within 4Å: Chain D: G.41, A.42, E.164, D.242, D.310, K.335, H.363, R.364, S.365, K.386 Ligands: CA.19, CA.20 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:A.42, D:S.365, D:S.365 Water bridges: D:E.164, D:D.310, D:K.335 Salt bridges: D:K.335, D:K.335, D:R.364, D:K.386 PEP.23: 14 residues within 4Å: Chain E: G.41, A.42, E.164, D.242, E.283, D.310, L.333, K.335, H.363, R.364, S.365, K.386 Ligands: CA.24, CA.25 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:D.242, E:S.365 Water bridges: E:E.164, E:D.310, E:D.310, E:K.335, E:K.335, E:H.363 Salt bridges: E:K.335, E:K.335, E:R.364, E:K.386 PEP.29: 12 residues within 4Å: Chain F: G.41, A.42, E.164, D.242, D.310, K.335, H.363, R.364, S.365, K.386 Ligands: CA.30, CA.31 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:A.42, F:S.365, F:S.365 Water bridges: F:E.164, F:D.310, F:K.335 Salt bridges: F:K.335, F:K.335, F:R.364, F:K.386 PEP.34: 14 residues within 4Å: Chain G: G.41, A.42, E.164, D.242, E.283, D.310, L.333, K.335, H.363, R.364, S.365, K.386 Ligands: CA.35, CA.36 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:D.242, G:S.365 Water bridges: G:E.164, G:D.310, G:D.310, G:K.335, G:K.335, G:H.363 Salt bridges: G:K.335, G:K.335, G:R.364, G:K.386 PEP.40: 12 residues within 4Å: Chain H: G.41, A.42, E.164, D.242, D.310, K.335, H.363, R.364, S.365, K.386 Ligands: CA.41, CA.42 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:A.42, H:S.365, H:S.365 Water bridges: H:E.164, H:D.310, H:K.335 Salt bridges: H:K.335, H:K.335, H:R.364, H:K.386

28 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.242, E.283, D.310, K.386 Ligands: PEP.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.242, A:E.283, A:D.310, H2O.1, H2O.4 CA.3: 2 residues within 4Å: Chain A: A.42 Ligands: PEP.1 5 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:A.42, H2O.1, H2O.2, H2O.4, PEP.1 CA.4: 2 residues within 4Å: Chain A: G.153, N.158 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:N.158, H2O.3, H2O.4, H2O.4 CA.5: 2 residues within 4Å: Chain A: T.44, E.288 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.44, A:E.288, A:E.288, H2O.3, H2O.4 CA.8: 4 residues within 4Å: Chain B: D.242, E.283, D.310 Ligands: PEP.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.242, B:E.283, B:D.310, H2O.5, H2O.7 CA.9: 3 residues within 4Å: Chain B: A.42, R.364 Ligands: PEP.7 6 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:A.42, H2O.6, H2O.7, H2O.8, H2O.8, PEP.7 CA.10: 3 residues within 4Å: Chain B: T.44, G.45, E.288 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.44, B:E.288 CA.13: 5 residues within 4Å: Chain C: D.242, E.283, D.310, K.386 Ligands: PEP.12 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.242, C:E.283, C:D.310, H2O.8, H2O.11 CA.14: 2 residues within 4Å: Chain C: A.42 Ligands: PEP.12 5 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: C:A.42, H2O.9, H2O.10, H2O.11, PEP.12 CA.15: 2 residues within 4Å: Chain C: G.153, N.158 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:N.158, H2O.11, H2O.11, H2O.12 CA.16: 2 residues within 4Å: Chain C: T.44, E.288 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.44, C:E.288, C:E.288, H2O.11, H2O.11 CA.19: 4 residues within 4Å: Chain D: D.242, E.283, D.310 Ligands: PEP.18 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.242, D:E.283, D:D.310, H2O.13, H2O.14 CA.20: 3 residues within 4Å: Chain D: A.42, R.364 Ligands: PEP.18 6 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: D:A.42, H2O.13, H2O.14, H2O.15, H2O.15, PEP.18 CA.21: 3 residues within 4Å: Chain D: T.44, G.45, E.288 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.44, D:E.288 CA.24: 5 residues within 4Å: Chain E: D.242, E.283, D.310, K.386 Ligands: PEP.23 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.242, E:E.283, E:D.310, H2O.16, H2O.18 CA.25: 2 residues within 4Å: Chain E: A.42 Ligands: PEP.23 5 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: E:A.42, H2O.16, H2O.17, H2O.18, PEP.23 CA.26: 2 residues within 4Å: Chain E: G.153, N.158 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:N.158, H2O.18, H2O.19, H2O.19 CA.27: 2 residues within 4Å: Chain E: T.44, E.288 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:T.44, E:E.288, E:E.288, H2O.18, H2O.19 CA.30: 4 residues within 4Å: Chain F: D.242, E.283, D.310 Ligands: PEP.29 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.242, F:E.283, F:D.310, H2O.20, H2O.21 CA.31: 3 residues within 4Å: Chain F: A.42, R.364 Ligands: PEP.29 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:A.42, H2O.21, H2O.22, H2O.22, H2O.22 CA.32: 3 residues within 4Å: Chain F: T.44, G.45, E.288 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.44, F:E.288 CA.35: 5 residues within 4Å: Chain G: D.242, E.283, D.310, K.386 Ligands: PEP.34 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.242, G:E.283, G:D.310, H2O.23, H2O.26 CA.36: 2 residues within 4Å: Chain G: A.42 Ligands: PEP.34 5 PLIP interactions: 1 interactions with chain G, 3 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: G:A.42, H2O.23, H2O.24, H2O.26, PEP.34 CA.37: 2 residues within 4Å: Chain G: G.153, N.158 4 PLIP interactions: 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:N.158, H2O.26, H2O.26, H2O.27 CA.38: 2 residues within 4Å: Chain G: T.44, E.288 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:T.44, G:E.288, G:E.288, H2O.25, H2O.26 CA.41: 4 residues within 4Å: Chain H: D.242, E.283, D.310 Ligands: PEP.40 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.242, H:E.283, H:D.310, H2O.28, H2O.29 CA.42: 3 residues within 4Å: Chain H: A.42, R.364 Ligands: PEP.40 6 PLIP interactions: 1 interactions with chain H, 4 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H:A.42, H2O.28, H2O.29, H2O.30, H2O.30, PEP.40 CA.43: 3 residues within 4Å: Chain H: T.44, G.45, E.288 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:T.44, H:E.288

8 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 3 residues within 4Å: Chain A: R.381, L.414 Chain H: R.347 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain A Salt bridges: H:R.347, A:R.381 Hydrophobic interactions: A:L.414 ACT.11: 3 residues within 4Å: Chain B: R.381, L.414 Chain E: R.347 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B Salt bridges: E:R.347, B:R.381 ACT.17: 3 residues within 4Å: Chain C: R.381, L.414 Chain F: R.347 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain F Hydrophobic interactions: C:L.414 Salt bridges: C:R.381, F:R.347 ACT.22: 3 residues within 4Å: Chain D: R.381, L.414 Chain G: R.347 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain G Salt bridges: D:R.381, G:R.347 ACT.28: 3 residues within 4Å: Chain B: R.347 Chain E: R.381, L.414 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: E:L.414 Salt bridges: E:R.381, B:R.347 ACT.33: 3 residues within 4Å: Chain C: R.347 Chain F: R.381, L.414 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C Salt bridges: F:R.381, C:R.347 ACT.39: 3 residues within 4Å: Chain D: R.347 Chain G: R.381, L.414 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain G Salt bridges: D:R.347, G:R.381 Hydrophobic interactions: G:L.414 ACT.44: 3 residues within 4Å: Chain A: R.347 Chain H: R.381, L.414 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain H Salt bridges: A:R.347, H:R.381

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gonzalez, J.M. et al., The structure of Synechococcus elongatus enolase reveals key aspects of phosphoenolpyruvate binding. Acta Crystallogr.,Sect.F (2022)

Release Date

2016-04-20

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

Related Entries With Identical Sequence