SMTL ID : 7e4f.1

Mycobacterium tuberculosis enolase mutant - E204A 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.47, A.48, S.49, Q.169, E.170, D.248, E.290, D.317, K.342, H.370, R.371, S.372, K.393 Ligands: MG.7 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:A.48, A:S.49, A:Q.169, A:S.372, A:S.372 Salt bridges: A:K.342, A:K.342, A:R.371, A:K.393 PEP.8: 14 residues within 4Å: Chain B: G.47, A.48, S.49, Q.169, E.170, D.248, E.290, D.317, K.342, H.370, R.371, S.372, K.393 Ligands: MG.14 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:A.48, B:S.49, B:Q.169, B:S.372, B:S.372 Salt bridges: B:K.342, B:K.342, B:R.371, B:K.393 PEP.15: 14 residues within 4Å: Chain C: G.47, A.48, S.49, Q.169, E.170, D.248, E.290, D.317, K.342, H.370, R.371, S.372, K.393 Ligands: MG.21 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:A.48, C:S.49, C:Q.169, C:S.372, C:S.372 Salt bridges: C:K.342, C:K.342, C:R.371, C:K.393 PEP.22: 14 residues within 4Å: Chain D: G.47, A.48, S.49, Q.169, E.170, D.248, E.290, D.317, K.342, H.370, R.371, S.372, K.393 Ligands: MG.28 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:A.48, D:S.49, D:Q.169, D:S.372, D:S.372 Salt bridges: D:K.342, D:K.342, D:R.371, D:K.393 PEP.29: 14 residues within 4Å: Chain E: G.47, A.48, S.49, Q.169, E.170, D.248, E.290, D.317, K.342, H.370, R.371, S.372, K.393 Ligands: MG.35 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:A.48, E:S.49, E:Q.169, E:D.248, E:S.372, E:S.372 Salt bridges: E:K.342, E:K.342, E:R.371, E:K.393 PEP.36: 14 residues within 4Å: Chain F: G.47, A.48, S.49, Q.169, E.170, D.248, E.290, D.317, K.342, H.370, R.371, S.372, K.393 Ligands: MG.42 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:A.48, F:S.49, F:Q.169, F:D.248, F:S.372, F:S.372 Salt bridges: F:K.342, F:K.342, F:R.371, F:K.393 PEP.43: 14 residues within 4Å: Chain G: G.47, A.48, S.49, Q.169, E.170, D.248, E.290, D.317, K.342, H.370, R.371, S.372, K.393 Ligands: MG.49 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:A.48, G:S.49, G:Q.169, G:D.248, G:S.372, G:S.372 Salt bridges: G:K.342, G:K.342, G:R.371, G:K.393 PEP.50: 14 residues within 4Å: Chain H: G.47, A.48, S.49, Q.169, E.170, D.248, E.290, D.317, K.342, H.370, R.371, S.372, K.393 Ligands: MG.56 10 PLIP interactions: 10 interactions with chain H Hydrogen bonds: H:A.48, H:S.49, H:Q.169, H:D.248, H:S.372, H:S.372 Salt bridges: H:K.342, H:K.342, H:R.371, H:K.393

16 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 Ligand excluded by PLIP PEG.3: 5 residues within 4Å: Chain A: R.186, W.187, E.190, A.235, L.237 Ligand excluded by PLIP PEG.9: 5 residues within 4Å: Chain B: P.83, A.84, I.86, G.87, L.88 Ligand excluded by PLIP PEG.10: 5 residues within 4Å: Chain B: R.186, W.187, E.190, A.235, L.237 Ligand excluded by PLIP PEG.16: 5 residues within 4Å: Chain C: P.83, A.84, I.86, G.87, L.88 Ligand excluded by PLIP PEG.17: 5 residues within 4Å: Chain C: R.186, W.187, E.190, A.235, L.237 Ligand excluded by PLIP PEG.23: 5 residues within 4Å: Chain D: P.83, A.84, I.86, G.87, L.88 Ligand excluded by PLIP PEG.24: 5 residues within 4Å: Chain D: R.186, W.187, E.190, A.235, L.237 Ligand excluded by PLIP PEG.30: 5 residues within 4Å: Chain E: P.83, A.84, I.86, G.87, L.88 Ligand excluded by PLIP PEG.31: 5 residues within 4Å: Chain E: R.186, W.187, E.190, A.235, L.237 Ligand excluded by PLIP PEG.37: 5 residues within 4Å: Chain F: P.83, A.84, I.86, G.87, L.88 Ligand excluded by PLIP PEG.38: 5 residues within 4Å: Chain F: R.186, W.187, E.190, A.235, L.237 Ligand excluded by PLIP PEG.44: 5 residues within 4Å: Chain G: P.83, A.84, I.86, G.87, L.88 Ligand excluded by PLIP PEG.45: 5 residues within 4Å: Chain G: R.186, W.187, E.190, A.235, L.237 Ligand excluded by PLIP PEG.51: 5 residues within 4Å: Chain H: P.83, A.84, I.86, G.87, L.88 Ligand excluded by PLIP PEG.52: 5 residues within 4Å: Chain H: R.186, W.187, E.190, A.235, L.237 Ligand excluded by PLIP

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

EDO.4: 4 residues within 4Å: Chain A: V.356, T.357 Chain H: G.141 Ligands: EDO.53 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.357 EDO.11: 4 residues within 4Å: Chain B: V.356, T.357 Chain G: G.141 Ligands: EDO.46 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.357 EDO.18: 4 residues within 4Å: Chain C: V.356, T.357 Chain F: G.141 Ligands: EDO.39 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.357 EDO.25: 4 residues within 4Å: Chain D: V.356, T.357 Chain E: G.141 Ligands: EDO.32 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.357 EDO.32: 4 residues within 4Å: Chain D: G.141 Chain E: V.356, T.357 Ligands: EDO.25 No protein-ligand interaction detected (PLIP) EDO.39: 4 residues within 4Å: Chain C: G.141 Chain F: V.356, T.357 Ligands: EDO.18 No protein-ligand interaction detected (PLIP) EDO.46: 4 residues within 4Å: Chain B: G.141 Chain G: V.356, T.357 Ligands: EDO.11 No protein-ligand interaction detected (PLIP) EDO.53: 4 residues within 4Å: Chain A: G.141 Chain H: V.356, T.357 Ligands: EDO.4 No protein-ligand interaction detected (PLIP)

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

ACT.5: 4 residues within 4Å: Chain A: Q.98, V.101, T.350, E.351 Ligand excluded by PLIP ACT.6: 2 residues within 4Å: Chain A: R.41 Chain E: Q.408 Ligand excluded by PLIP ACT.12: 4 residues within 4Å: Chain B: Q.98, V.101, T.350, E.351 Ligand excluded by PLIP ACT.13: 2 residues within 4Å: Chain B: R.41 Chain F: Q.408 Ligand excluded by PLIP ACT.19: 4 residues within 4Å: Chain C: Q.98, V.101, T.350, E.351 Ligand excluded by PLIP ACT.20: 2 residues within 4Å: Chain C: R.41 Chain H: Q.408 Ligand excluded by PLIP ACT.26: 4 residues within 4Å: Chain D: Q.98, V.101, T.350, E.351 Ligand excluded by PLIP ACT.27: 2 residues within 4Å: Chain D: R.41 Chain G: Q.408 Ligand excluded by PLIP ACT.33: 4 residues within 4Å: Chain E: Q.98, V.101, T.350, E.351 Ligand excluded by PLIP ACT.34: 2 residues within 4Å: Chain A: Q.408 Chain E: R.41 Ligand excluded by PLIP ACT.40: 4 residues within 4Å: Chain F: Q.98, V.101, T.350, E.351 Ligand excluded by PLIP ACT.41: 2 residues within 4Å: Chain B: Q.408 Chain F: R.41 Ligand excluded by PLIP ACT.47: 4 residues within 4Å: Chain G: Q.98, V.101, T.350, E.351 Ligand excluded by PLIP ACT.48: 2 residues within 4Å: Chain D: Q.408 Chain G: R.41 Ligand excluded by PLIP ACT.54: 4 residues within 4Å: Chain H: Q.98, V.101, T.350, E.351 Ligand excluded by PLIP ACT.55: 2 residues within 4Å: Chain C: Q.408 Chain H: R.41 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.2 MG.14: 5 residues within 4Å: Chain B: D.248, E.290, D.317, K.393 Ligands: PEP.8 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.7 MG.21: 5 residues within 4Å: Chain C: D.248, E.290, D.317, K.393 Ligands: PEP.15 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.13 MG.28: 5 residues within 4Å: Chain D: D.248, E.290, D.317, K.393 Ligands: PEP.22 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.248, D:E.290, D:D.317, H2O.18, H2O.18 MG.35: 5 residues within 4Å: Chain E: D.248, E.290, D.317, K.393 Ligands: PEP.29 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.24 MG.42: 5 residues within 4Å: Chain F: D.248, E.290, D.317, K.393 Ligands: PEP.36 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.248, F:E.290, F:D.317, H2O.29, H2O.29 MG.49: 5 residues within 4Å: Chain G: D.248, E.290, D.317, K.393 Ligands: PEP.43 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.248, G:E.290, G:D.317, H2O.34, H2O.35 MG.56: 5 residues within 4Å: Chain H: D.248, E.290, D.317, K.393 Ligands: PEP.50 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.248, H:E.290, H:D.317, H2O.40, H2O.40

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
A

C
A

D
A

E
A

F
A

G
A

H
A

Enolase