SMTL ID : 7e51.1

Structure of PEP bound Enolase from Mycobacterium tuberculosis

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-octamer

Ligands

8 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.1: 14 residues within 4Å: Chain A: G.47, A.48, S.49, E.170, E.211, D.317, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.2, MG.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.48, A:S.369, A:S.372 Salt bridges: A:K.342, A:K.342, A:R.371, A:K.393 PEP.4: 14 residues within 4Å: Chain B: G.47, A.48, E.170, E.211, E.290, D.317, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.5, MG.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:A.48, B:S.369, B:S.369, B:S.372 Salt bridges: B:K.342, B:K.342, B:R.371, B:K.393 PEP.7: 15 residues within 4Å: Chain C: G.47, A.48, S.49, E.170, E.211, D.248, E.290, D.317, K.342, H.370, R.371, S.372, K.393 Ligands: MG.8, MG.9 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:A.48, C:S.369, C:S.372 Salt bridges: C:K.342, C:K.342, C:R.371, C:K.393 PEP.10: 12 residues within 4Å: Chain D: G.47, A.48, E.170, E.290, D.317, K.342, H.370, R.371, S.372, K.393 Ligands: MG.11, MG.12 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:A.48, D:S.369, D:S.372 Salt bridges: D:K.342, D:K.342, D:R.371, D:K.393 PEP.13: 16 residues within 4Å: Chain E: G.47, A.48, S.49, E.170, E.211, D.248, E.290, D.317, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.14, MG.15 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:A.48, E:S.369, E:S.372 Salt bridges: E:K.342, E:K.342, E:R.371, E:K.393 PEP.16: 16 residues within 4Å: Chain F: G.47, A.48, S.49, E.170, E.211, D.248, E.290, D.317, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.17, MG.18 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:A.48, F:S.49, F:S.369, F:S.369, F:S.372 Salt bridges: F:K.342, F:K.342, F:R.371, F:K.393 PEP.19: 16 residues within 4Å: Chain G: G.47, A.48, S.49, E.170, E.211, D.248, E.290, D.317, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.20, MG.21 7 PLIP interactions: 7 interactions with chain G Hydrogen bonds: G:A.48, G:S.369, G:S.372 Salt bridges: G:K.342, G:K.342, G:R.371, G:K.393 PEP.22: 15 residues within 4Å: Chain H: G.47, A.48, S.49, E.170, E.211, E.290, D.317, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.23, MG.24 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:A.48, H:S.369, H:S.372 Salt bridges: H:K.342, H:K.342, H:R.371, H:K.393

16 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.49, D.317, K.342 Ligands: PEP.1 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:S.49, PEP.1 MG.3: 4 residues within 4Å: Chain A: D.248, E.290, D.317 Ligands: PEP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.248, A:E.290, A:D.317 MG.5: 2 residues within 4Å: Chain B: S.49 Ligands: PEP.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:S.49, B:S.49, PEP.4 MG.6: 5 residues within 4Å: Chain B: D.248, E.290, D.291, D.317 Ligands: PEP.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.290, B:D.317 MG.8: 2 residues within 4Å: Chain C: S.49 Ligands: PEP.7 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:S.49, PEP.7 MG.9: 4 residues within 4Å: Chain C: D.248, E.290, D.317 Ligands: PEP.7 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.248, C:D.248, C:E.290, C:D.317 MG.11: 2 residues within 4Å: Chain D: S.49 Ligands: PEP.10 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Ligand interactions Metal complexes: D:S.49, PEP.10 MG.12: 5 residues within 4Å: Chain D: Q.169, D.248, E.290, D.317 Ligands: PEP.10 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.248, D:E.290, D:D.317 MG.14: 3 residues within 4Å: Chain E: S.49, K.342 Ligands: PEP.13 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:S.49, PEP.13 MG.15: 4 residues within 4Å: Chain E: D.248, E.290, D.317 Ligands: PEP.13 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.248, E:E.290, E:D.317 MG.17: 2 residues within 4Å: Chain F: S.49 Ligands: PEP.16 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:S.49, F:S.49, PEP.16 MG.18: 4 residues within 4Å: Chain F: D.248, E.290, D.317 Ligands: PEP.16 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.248, F:E.290, F:D.317 MG.20: 2 residues within 4Å: Chain G: S.49 Ligands: PEP.19 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Ligand interactions Metal complexes: G:S.49, PEP.19 MG.21: 4 residues within 4Å: Chain G: D.248, E.290, D.317 Ligands: PEP.19 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.248, G:E.290, G:D.317 MG.23: 2 residues within 4Å: Chain H: S.49 Ligands: PEP.22 2 PLIP interactions: 1 interactions with chain H, 1 Ligand-Ligand interactions Metal complexes: H:S.49, PEP.22 MG.24: 4 residues within 4Å: Chain H: D.248, E.290, D.317 Ligands: PEP.22 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:D.248, H:E.290, H:D.317

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahmad, M. et al., Structural snapshots of Mycobacterium tuberculosis enolase reveal dual mode of 2PG binding and its implication in enzyme catalysis. Iucrj (2023)

Release Date

2022-02-16

Peptides

Enolase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Enolase

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