SMTL ID : 6l7d.1

Mycobacterium tuberculosis enolase mutant - S42A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-octamer

Ligands

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

EDO.1: 1 residues within 4Å: Chain A: R.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.41 EDO.5: 1 residues within 4Å: Chain B: R.41 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.41 EDO.9: 1 residues within 4Å: Chain C: R.41 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.41 EDO.13: 1 residues within 4Å: Chain D: R.41 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.41 EDO.17: 1 residues within 4Å: Chain E: R.41 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.41 EDO.21: 1 residues within 4Å: Chain F: R.41 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.41 EDO.25: 1 residues within 4Å: Chain G: R.41 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.41 EDO.29: 1 residues within 4Å: Chain H: R.41 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:R.41

8 x 2PG: 2-PHOSPHOGLYCERIC ACID(Non-covalent)

2PG.2: 18 residues within 4Å: Chain A: G.47, A.48, A.49, H.161, Q.169, E.170, E.211, D.248, E.290, D.317, L.340, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:A.48, A:A.49, A:H.370, A:S.372, A:S.372, A:K.393 Water bridges: A:K.342, A:K.342 Salt bridges: A:H.161, A:K.342, A:K.342, A:R.371, A:K.393 2PG.6: 18 residues within 4Å: Chain B: G.47, A.48, A.49, H.161, Q.169, E.170, E.211, D.248, E.290, D.317, L.340, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.8 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:A.48, B:A.49, B:H.370, B:S.372, B:S.372, B:K.393 Water bridges: B:K.342, B:K.342 Salt bridges: B:H.161, B:K.342, B:K.342, B:R.371, B:K.393 2PG.10: 18 residues within 4Å: Chain C: G.47, A.48, A.49, H.161, Q.169, E.170, E.211, D.248, E.290, D.317, L.340, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.12 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:A.48, C:A.49, C:H.370, C:S.372, C:S.372, C:K.393 Water bridges: C:K.342, C:K.342 Salt bridges: C:H.161, C:K.342, C:K.342, C:R.371, C:K.393 2PG.14: 18 residues within 4Å: Chain D: G.47, A.48, A.49, H.161, Q.169, E.170, E.211, D.248, E.290, D.317, L.340, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.16 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:A.48, D:A.49, D:Q.169, D:H.370, D:S.372, D:S.372, D:K.393 Water bridges: D:K.342, D:K.342 Salt bridges: D:H.161, D:K.342, D:K.342, D:R.371, D:K.393 2PG.18: 18 residues within 4Å: Chain E: G.47, A.48, A.49, H.161, Q.169, E.170, E.211, D.248, E.290, D.317, L.340, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.20 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:A.48, E:A.49, E:D.248, E:H.370, E:S.372, E:S.372, E:K.393 Water bridges: E:K.342, E:K.342 Salt bridges: E:H.161, E:K.342, E:K.342, E:R.371, E:K.393 2PG.22: 18 residues within 4Å: Chain F: G.47, A.48, A.49, H.161, Q.169, E.170, E.211, D.248, E.290, D.317, L.340, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.24 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:A.48, F:A.49, F:D.248, F:H.370, F:S.372, F:S.372, F:K.393 Water bridges: F:K.342, F:K.342 Salt bridges: F:H.161, F:K.342, F:K.342, F:R.371, F:K.393 2PG.26: 18 residues within 4Å: Chain G: G.47, A.48, A.49, H.161, Q.169, E.170, E.211, D.248, E.290, D.317, L.340, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.28 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:A.48, G:A.49, G:D.248, G:H.370, G:S.372, G:S.372, G:K.393 Water bridges: G:K.342, G:K.342 Salt bridges: G:H.161, G:K.342, G:K.342, G:R.371, G:K.393 2PG.30: 18 residues within 4Å: Chain H: G.47, A.48, A.49, H.161, Q.169, E.170, E.211, D.248, E.290, D.317, L.340, K.342, S.369, H.370, R.371, S.372, K.393 Ligands: MG.32 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:A.48, H:A.49, H:Q.169, H:D.248, H:H.370, H:S.372, H:S.372, H:K.393 Water bridges: H:K.342, H:K.342 Salt bridges: H:H.161, H:K.342, H:K.342, H:R.371, H:K.393

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

ACT.3: 1 residues within 4Å: Chain A: D.354 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain A Salt bridges: H:R.421, A:R.94 Hydrogen bonds: A:D.354 ACT.7: 1 residues within 4Å: Chain B: D.354 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain G Hydrogen bonds: B:D.354 Salt bridges: B:R.94, G:R.421 ACT.11: 1 residues within 4Å: Chain C: D.354 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:D.354 Salt bridges: C:R.94, F:R.421 ACT.15: 1 residues within 4Å: Chain D: D.354 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Salt bridges: E:R.421, D:R.94 Hydrogen bonds: D:D.354 ACT.19: 1 residues within 4Å: Chain E: D.354 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Salt bridges: D:R.421, E:R.94 ACT.23: 1 residues within 4Å: Chain F: D.354 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain C Salt bridges: F:R.94, C:R.421 ACT.27: 1 residues within 4Å: Chain G: D.354 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain B Salt bridges: G:R.94, B:R.421 ACT.31: 1 residues within 4Å: Chain H: D.354 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain H Salt bridges: A:R.421, H:R.94

8 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 6 residues within 4Å: Chain A: D.248, A.250, E.290, D.291, D.317 Ligands: 2PG.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.248, A:D.317 MG.8: 6 residues within 4Å: Chain B: D.248, A.250, E.290, D.291, D.317 Ligands: 2PG.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.248, B:D.317 MG.12: 6 residues within 4Å: Chain C: D.248, A.250, E.290, D.291, D.317 Ligands: 2PG.10 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.248, C:D.317 MG.16: 6 residues within 4Å: Chain D: D.248, A.250, E.290, D.291, D.317 Ligands: 2PG.14 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.248, D:D.317 MG.20: 6 residues within 4Å: Chain E: D.248, A.250, E.290, D.291, D.317 Ligands: 2PG.18 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.248, E:D.317 MG.24: 6 residues within 4Å: Chain F: D.248, A.250, E.290, D.291, D.317 Ligands: 2PG.22 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.248, F:D.317 MG.28: 6 residues within 4Å: Chain G: D.248, A.250, E.290, D.291, D.317 Ligands: 2PG.26 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.248, G:D.317 MG.32: 6 residues within 4Å: Chain H: D.248, A.250, E.290, D.291, D.317 Ligands: 2PG.30 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.248, 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

2020-11-04

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