SMTL ID : 7dlr.1

Mycobacterium tuberculosis enolase mutant - E163A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-octamer

Ligands

8 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.1: 16 residues within 4Å: Chain A: G.47, A.48, S.49, Q.169, E.211, D.248, E.290, D.317, L.340, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.7 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:A.48, A:Q.169, A:S.369, A:S.372, A:S.372 Water bridges: A:E.290, A:K.342, A:K.342, A:K.342, A:R.371, A:R.371 Salt bridges: A:K.342, A:K.342, A:R.371, A:K.393 PEP.12: 16 residues within 4Å: Chain B: G.47, A.48, S.49, Q.169, E.211, D.248, E.290, D.317, L.340, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.18 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:A.48, B:Q.169, B:S.369, B:S.372, B:S.372 Water bridges: B:E.290, B:K.342, B:K.342, B:K.342, B:R.371, B:R.371 Salt bridges: B:K.342, B:K.342, B:R.371, B:K.393 PEP.23: 16 residues within 4Å: Chain C: G.47, A.48, S.49, Q.169, E.211, D.248, E.290, D.317, L.340, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.29 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:A.48, C:Q.169, C:S.369, C:S.372, C:S.372 Water bridges: C:E.290, C:K.342, C:K.342, C:K.342, C:R.371, C:R.371 Salt bridges: C:K.342, C:K.342, C:R.371, C:K.393 PEP.34: 16 residues within 4Å: Chain D: G.47, A.48, S.49, Q.169, E.211, D.248, E.290, D.317, L.340, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.40 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:A.48, D:Q.169, D:S.369, D:S.372, D:S.372 Water bridges: D:E.290, D:K.342, D:K.342, D:K.342, D:R.371, D:R.371 Salt bridges: D:K.342, D:K.342, D:R.371, D:K.393 PEP.45: 16 residues within 4Å: Chain E: G.47, A.48, S.49, Q.169, E.211, D.248, E.290, D.317, L.340, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.51 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:A.48, E:Q.169, E:D.248, E:D.317, E:S.369, E:S.372, E:S.372 Water bridges: E:K.342, E:K.342, E:K.342, E:R.371, E:R.371 Salt bridges: E:K.342, E:K.342, E:R.371, E:K.393 PEP.56: 16 residues within 4Å: Chain F: G.47, A.48, S.49, Q.169, E.211, D.248, E.290, D.317, L.340, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.62 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:A.48, F:Q.169, F:D.248, F:D.317, F:S.369, F:S.372, F:S.372 Water bridges: F:K.342, F:K.342, F:K.342, F:R.371, F:R.371 Salt bridges: F:K.342, F:K.342, F:R.371, F:K.393 PEP.67: 16 residues within 4Å: Chain G: G.47, A.48, S.49, Q.169, E.211, D.248, E.290, D.317, L.340, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.73 16 PLIP interactions: 16 interactions with chain G Hydrogen bonds: G:A.48, G:Q.169, G:D.248, G:D.317, G:S.369, G:S.372, G:S.372 Water bridges: G:K.342, G:K.342, G:K.342, G:R.371, G:R.371 Salt bridges: G:K.342, G:K.342, G:R.371, G:K.393 PEP.78: 16 residues within 4Å: Chain H: G.47, A.48, S.49, Q.169, E.211, D.248, E.290, D.317, L.340, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.84 16 PLIP interactions: 16 interactions with chain H Hydrogen bonds: H:A.48, H:Q.169, H:D.248, H:D.317, H:S.369, H:S.372, H:S.372 Water bridges: H:K.342, H:K.342, H:K.342, H:R.371, H:R.371 Salt bridges: H:K.342, H:K.342, H:R.371, H:K.393

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain A: P.83, A.84, I.86, G.87, L.88 No protein-ligand interaction detected (PLIP) PEG.13: 5 residues within 4Å: Chain B: P.83, A.84, I.86, G.87, L.88 No protein-ligand interaction detected (PLIP) PEG.24: 5 residues within 4Å: Chain C: P.83, A.84, I.86, G.87, L.88 No protein-ligand interaction detected (PLIP) PEG.35: 5 residues within 4Å: Chain D: P.83, A.84, I.86, G.87, L.88 No protein-ligand interaction detected (PLIP) PEG.46: 5 residues within 4Å: Chain E: P.83, A.84, I.86, G.87, L.88 No protein-ligand interaction detected (PLIP) PEG.57: 5 residues within 4Å: Chain F: P.83, A.84, I.86, G.87, L.88 No protein-ligand interaction detected (PLIP) PEG.68: 5 residues within 4Å: Chain G: P.83, A.84, I.86, G.87, L.88 No protein-ligand interaction detected (PLIP) PEG.79: 5 residues within 4Å: Chain H: P.83, A.84, I.86, G.87, L.88 No protein-ligand interaction detected (PLIP)

24 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: R.186, W.187, E.190, A.235 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: P.179, S.180, E.413, A.420, R.421, Y.422 Ligands: EDO.10 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: A.178, Y.422, A.423, G.424, D.425, L.426 Ligands: EDO.4 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain B: R.186, W.187, E.190, A.235 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain B: P.179, S.180, E.413, A.420, R.421, Y.422 Ligands: EDO.21 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain B: A.178, Y.422, A.423, G.424, D.425, L.426 Ligands: EDO.15 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain C: R.186, W.187, E.190, A.235 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain C: P.179, S.180, E.413, A.420, R.421, Y.422 Ligands: EDO.32 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain C: A.178, Y.422, A.423, G.424, D.425, L.426 Ligands: EDO.26 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain D: R.186, W.187, E.190, A.235 Ligand excluded by PLIP EDO.37: 7 residues within 4Å: Chain D: P.179, S.180, E.413, A.420, R.421, Y.422 Ligands: EDO.43 Ligand excluded by PLIP EDO.43: 7 residues within 4Å: Chain D: A.178, Y.422, A.423, G.424, D.425, L.426 Ligands: EDO.37 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain E: R.186, W.187, E.190, A.235 Ligand excluded by PLIP EDO.48: 7 residues within 4Å: Chain E: P.179, S.180, E.413, A.420, R.421, Y.422 Ligands: EDO.54 Ligand excluded by PLIP EDO.54: 7 residues within 4Å: Chain E: A.178, Y.422, A.423, G.424, D.425, L.426 Ligands: EDO.48 Ligand excluded by PLIP EDO.58: 4 residues within 4Å: Chain F: R.186, W.187, E.190, A.235 Ligand excluded by PLIP EDO.59: 7 residues within 4Å: Chain F: P.179, S.180, E.413, A.420, R.421, Y.422 Ligands: EDO.65 Ligand excluded by PLIP EDO.65: 7 residues within 4Å: Chain F: A.178, Y.422, A.423, G.424, D.425, L.426 Ligands: EDO.59 Ligand excluded by PLIP EDO.69: 4 residues within 4Å: Chain G: R.186, W.187, E.190, A.235 Ligand excluded by PLIP EDO.70: 7 residues within 4Å: Chain G: P.179, S.180, E.413, A.420, R.421, Y.422 Ligands: EDO.76 Ligand excluded by PLIP EDO.76: 7 residues within 4Å: Chain G: A.178, Y.422, A.423, G.424, D.425, L.426 Ligands: EDO.70 Ligand excluded by PLIP EDO.80: 4 residues within 4Å: Chain H: R.186, W.187, E.190, A.235 Ligand excluded by PLIP EDO.81: 7 residues within 4Å: Chain H: P.179, S.180, E.413, A.420, R.421, Y.422 Ligands: EDO.87 Ligand excluded by PLIP EDO.87: 7 residues within 4Å: Chain H: A.178, Y.422, A.423, G.424, D.425, L.426 Ligands: EDO.81 Ligand excluded by PLIP

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

ACT.5: 3 residues within 4Å: Chain A: Q.408, A.415 Chain E: R.41 Ligand excluded by PLIP ACT.6: 2 residues within 4Å: Chain A: T.357, H.360 Ligand excluded by PLIP ACT.16: 3 residues within 4Å: Chain B: Q.408, A.415 Chain F: R.41 Ligand excluded by PLIP ACT.17: 2 residues within 4Å: Chain B: T.357, H.360 Ligand excluded by PLIP ACT.27: 3 residues within 4Å: Chain C: Q.408, A.415 Chain H: R.41 Ligand excluded by PLIP ACT.28: 2 residues within 4Å: Chain C: T.357, H.360 Ligand excluded by PLIP ACT.38: 3 residues within 4Å: Chain D: Q.408, A.415 Chain G: R.41 Ligand excluded by PLIP ACT.39: 2 residues within 4Å: Chain D: T.357, H.360 Ligand excluded by PLIP ACT.49: 3 residues within 4Å: Chain A: R.41 Chain E: Q.408, A.415 Ligand excluded by PLIP ACT.50: 2 residues within 4Å: Chain E: T.357, H.360 Ligand excluded by PLIP ACT.60: 3 residues within 4Å: Chain B: R.41 Chain F: Q.408, A.415 Ligand excluded by PLIP ACT.61: 2 residues within 4Å: Chain F: T.357, H.360 Ligand excluded by PLIP ACT.71: 3 residues within 4Å: Chain D: R.41 Chain G: Q.408, A.415 Ligand excluded by PLIP ACT.72: 2 residues within 4Å: Chain G: T.357, H.360 Ligand excluded by PLIP ACT.82: 3 residues within 4Å: Chain C: R.41 Chain H: Q.408, A.415 Ligand excluded by PLIP ACT.83: 2 residues within 4Å: Chain H: T.357, H.360 Ligand excluded by PLIP

8 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 5 residues within 4Å: Chain A: D.248, E.290, D.317, K.393 Ligands: PEP.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.248, A:E.290, A:D.317, H2O.1, H2O.4 MG.18: 5 residues within 4Å: Chain B: D.248, E.290, D.317, K.393 Ligands: PEP.12 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.248, B:E.290, B:D.317, H2O.7, H2O.9 MG.29: 5 residues within 4Å: Chain C: D.248, E.290, D.317, K.393 Ligands: PEP.23 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.248, C:E.290, C:D.317, H2O.12, H2O.15 MG.40: 5 residues within 4Å: Chain D: D.248, E.290, D.317, K.393 Ligands: PEP.34 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.248, D:E.290, D:D.317, H2O.17, H2O.20 MG.51: 5 residues within 4Å: Chain E: D.248, E.290, D.317, K.393 Ligands: PEP.45 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.248, E:E.290, E:D.317, H2O.23, H2O.25 MG.62: 5 residues within 4Å: Chain F: D.248, E.290, D.317, K.393 Ligands: PEP.56 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.248, F:E.290, F:D.317, H2O.28, H2O.30 MG.73: 5 residues within 4Å: Chain G: D.248, E.290, D.317, K.393 Ligands: PEP.67 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.248, G:E.290, G:D.317, H2O.33, H2O.36 MG.84: 5 residues within 4Å: Chain H: D.248, E.290, D.317, K.393 Ligands: PEP.78 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.248, H:E.290, H:D.317, H2O.38, H2O.41

24 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: H.360, R.365, T.366, S.389 Ligand excluded by PLIP CL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: H.360, R.365, T.366, S.389 Ligand excluded by PLIP CL.22: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain C: H.360, R.365, T.366, S.389 Ligand excluded by PLIP CL.33: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.41: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain D: H.360, R.365, T.366, S.389 Ligand excluded by PLIP CL.44: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.52: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.53: 4 residues within 4Å: Chain E: H.360, R.365, T.366, S.389 Ligand excluded by PLIP CL.55: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.63: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.64: 4 residues within 4Å: Chain F: H.360, R.365, T.366, S.389 Ligand excluded by PLIP CL.66: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.74: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.75: 4 residues within 4Å: Chain G: H.360, R.365, T.366, S.389 Ligand excluded by PLIP CL.77: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.85: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.86: 4 residues within 4Å: Chain H: H.360, R.365, T.366, S.389 Ligand excluded by PLIP CL.88: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

2021-12-01

Peptides

Enolase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

Enolase