SMTL ID : 7cll.1

Mycobacterium tubeculosis enolase in complex with 2-Phosphoglycerate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-octamer

Ligands

16 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: S.49, D.317, K.342 Ligands: MG.2, 2PG.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.49, A:S.49, H2O.1, H2O.5 MG.2: 7 residues within 4Å: Chain A: D.248, E.290, D.317, K.342, K.393 Ligands: MG.1, 2PG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.248, A:E.290, A:D.317, H2O.6 MG.6: 4 residues within 4Å: Chain B: S.49, D.317, K.342 Ligands: 2PG.8 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:S.49, B:S.49, 2PG.8, H2O.10, H2O.10 MG.7: 5 residues within 4Å: Chain B: D.248, E.290, D.317, K.393 Ligands: 2PG.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.248, B:E.290, B:D.317, H2O.11 MG.11: 7 residues within 4Å: Chain C: D.248, E.290, D.317, K.342, K.393 Ligands: MG.12, 2PG.13 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.248, C:E.290, C:D.317, H2O.20 MG.12: 5 residues within 4Å: Chain C: S.49, D.317, K.342 Ligands: MG.11, 2PG.13 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.49, C:S.49, H2O.20, H2O.22 MG.19: 3 residues within 4Å: Chain D: S.49, K.342 Ligands: 2PG.21 5 PLIP interactions: 2 interactions with chain D, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: D:S.49, D:S.49, 2PG.21, H2O.34, H2O.41 MG.20: 6 residues within 4Å: Chain D: D.248, E.290, D.317, K.342, K.393 Ligands: 2PG.21 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.248, D:E.290, D:D.317, H2O.35 MG.25: 5 residues within 4Å: Chain E: S.49, D.317, K.342 Ligands: MG.26, 2PG.27 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:S.49, E:S.49, H2O.44, H2O.49 MG.26: 7 residues within 4Å: Chain E: D.248, E.290, D.317, K.342, K.393 Ligands: MG.25, 2PG.27 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.248, E:E.290, E:D.317, H2O.50 MG.30: 4 residues within 4Å: Chain F: S.49, D.317, K.342 Ligands: 2PG.32 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:S.49, F:S.49, H2O.53, H2O.54 MG.31: 5 residues within 4Å: Chain F: D.248, E.290, D.317, K.393 Ligands: 2PG.32 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.248, F:E.290, F:D.317, H2O.55 MG.35: 7 residues within 4Å: Chain G: D.248, E.290, D.317, K.342, K.393 Ligands: MG.36, 2PG.37 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.248, G:E.290, G:D.317, H2O.64 MG.36: 5 residues within 4Å: Chain G: S.49, D.317, K.342 Ligands: MG.35, 2PG.37 4 PLIP interactions: 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:S.49, G:S.49, H2O.64, H2O.66 MG.43: 3 residues within 4Å: Chain H: S.49, K.342 Ligands: 2PG.45 5 PLIP interactions: 2 interactions with chain H, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: H:S.49, H:S.49, 2PG.45, H2O.78, H2O.84 MG.44: 6 residues within 4Å: Chain H: D.248, E.290, D.317, K.342, K.393 Ligands: 2PG.45 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.248, H:E.290, H:D.317, H2O.79

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

2PG.3: 18 residues within 4Å: Chain A: G.47, A.48, S.49, H.161, Q.169, E.170, E.211, D.248, E.290, D.317, L.340, K.342, H.370, R.371, S.372, K.393 Ligands: MG.1, MG.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:A.48, A:S.49, A:Q.169, A:H.370, A:S.372, A:S.372, A:K.393 Water bridges: A:N.154, A:E.290, A:R.371, A:R.371 Salt bridges: A:H.161, A:K.342, A:K.342, A:R.371, A:K.393 2PG.8: 18 residues within 4Å: Chain B: G.47, A.48, S.49, H.161, Q.169, E.170, E.211, D.248, E.290, D.317, L.340, K.342, H.370, R.371, S.372, K.393 Ligands: MG.6, MG.7 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:A.48, B:S.49, B:S.49, B:H.370, B:S.372 Water bridges: B:N.154, B:E.290, B:K.342, B:R.371 Salt bridges: B:H.161, B:K.342, B:K.342, B:R.371, B:K.393 2PG.13: 19 residues within 4Å: Chain C: G.47, A.48, S.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.11, MG.12 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:A.48, C:S.49, C:Q.169, C:H.370, C:S.372, C:S.372 Water bridges: C:E.54, C:N.154, C:R.371 Salt bridges: C:H.161, C:K.342, C:K.342, C:R.371, C:K.393 2PG.21: 19 residues within 4Å: Chain D: G.47, A.48, S.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.19, MG.20 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:A.48, D:S.49, D:S.49, D:S.49, D:Q.169, D:E.170, D:H.370, D:S.372, D:K.393 Water bridges: D:N.154, D:E.290, D:K.342, D:R.371 Salt bridges: D:H.161, D:K.342, D:K.342, D:R.371, D:K.393 2PG.27: 18 residues within 4Å: Chain E: G.47, A.48, S.49, H.161, Q.169, E.170, E.211, D.248, E.290, D.317, L.340, K.342, H.370, R.371, S.372, K.393 Ligands: MG.25, MG.26 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:A.48, E:S.49, E:Q.169, E:H.370, E:S.372, E:S.372, E:K.393 Water bridges: E:N.154, E:Q.345, E:R.371 Salt bridges: E:H.161, E:K.342, E:K.342, E:R.371, E:K.393 2PG.32: 18 residues within 4Å: Chain F: G.47, A.48, S.49, H.161, Q.169, E.170, E.211, D.248, E.290, D.317, L.340, K.342, H.370, R.371, S.372, K.393 Ligands: MG.30, MG.31 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:A.48, F:S.49, F:S.49, F:H.370, F:S.372 Water bridges: F:N.154, F:K.342, F:R.371 Salt bridges: F:H.161, F:K.342, F:K.342, F:R.371, F:K.393 2PG.37: 19 residues within 4Å: Chain G: G.47, A.48, S.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.35, MG.36 16 PLIP interactions: 16 interactions with chain G Hydrogen bonds: G:A.48, G:S.49, G:Q.169, G:E.170, G:H.370, G:S.372, G:S.372 Water bridges: G:E.54, G:N.154, G:E.290, G:K.342 Salt bridges: G:H.161, G:K.342, G:K.342, G:R.371, G:K.393 2PG.45: 19 residues within 4Å: Chain H: G.47, A.48, S.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.43, MG.44 16 PLIP interactions: 16 interactions with chain H Hydrogen bonds: H:A.48, H:S.49, H:S.49, H:S.49, H:Q.169, H:H.370, H:S.372, H:K.393 Water bridges: H:N.154, H:K.342, H:K.342 Salt bridges: H:H.161, H:K.342, H:K.342, H:R.371, H:K.393

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: R.23, N.25, K.68 Chain B: Y.192, H.193, K.196 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.196, A:N.25, A:K.68 Water bridges: B:Y.192, B:H.193, A:K.68 GOL.14: 2 residues within 4Å: Chain C: N.337, G.363 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.363 Water bridges: C:N.337 GOL.18: 7 residues within 4Å: Chain C: P.135, F.137, Q.408, R.411, I.412 Chain D: E.31, R.41 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.408, C:Q.408, D:E.31, D:R.41 Water bridges: C:R.411 GOL.28: 6 residues within 4Å: Chain E: R.23, N.25, K.68 Chain F: Y.192, H.193, K.196 7 PLIP interactions: 3 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:N.25, E:K.68, F:K.196 Water bridges: E:K.68, F:Y.192, F:Y.192, F:H.193 GOL.38: 2 residues within 4Å: Chain G: N.337, G.363 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.363 Water bridges: G:N.337 GOL.42: 7 residues within 4Å: Chain G: P.135, F.137, Q.408, R.411, I.412 Chain H: E.31, R.41 5 PLIP interactions: 2 interactions with chain H, 3 interactions with chain G Hydrogen bonds: H:E.31, H:R.41, G:Q.408, G:Q.408 Water bridges: G:R.411

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

ACT.5: 3 residues within 4Å: Chain A: P.135, Q.408 Chain B: R.41 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.408 Water bridges: A:R.411 ACT.9: 3 residues within 4Å: Chain B: R.94, Q.98, D.354 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.98, B:Q.98 ACT.10: 2 residues within 4Å: Chain B: K.201, R.230 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.201 Water bridges: B:S.234 Salt bridges: B:K.201, B:R.230 ACT.15: 5 residues within 4Å: Chain C: R.186, E.190, A.235, G.236, L.237 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.237 Hydrogen bonds: C:A.235 Water bridges: C:R.186, C:R.186 Salt bridges: C:R.186 ACT.16: 3 residues within 4Å: Chain C: V.198, K.201, R.230 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.198 Salt bridges: C:K.201, C:R.230 ACT.22: 2 residues within 4Å: Chain D: K.201, R.230 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.230 ACT.29: 3 residues within 4Å: Chain E: P.135, Q.408 Chain F: R.41 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.408 Water bridges: E:R.411 ACT.33: 3 residues within 4Å: Chain F: R.94, Q.98, D.354 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Q.98, F:Q.98, F:D.354 ACT.34: 2 residues within 4Å: Chain F: K.201, R.230 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:K.201 Water bridges: F:S.234 Salt bridges: F:K.201, F:R.230 ACT.39: 5 residues within 4Å: Chain G: R.186, E.190, A.235, G.236, L.237 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:L.237 Hydrogen bonds: G:A.235 Water bridges: G:R.186, G:R.186 Salt bridges: G:R.186 ACT.40: 3 residues within 4Å: Chain G: V.198, K.201, R.230 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:V.198 Salt bridges: G:K.201, G:R.230 ACT.46: 2 residues within 4Å: Chain H: K.201, R.230 1 PLIP interactions: 1 interactions with chain H Salt bridges: H:R.230

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

PEG.17: 4 residues within 4Å: Chain C: E.233, G.236, L.237, R.238 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.233 Water bridges: C:G.236 PEG.23: 5 residues within 4Å: Chain D: G.159, A.160, D.167, E.253, F.254 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.167, D:D.167, D:E.253 Water bridges: D:A.160, D:E.253, D:E.253 PEG.41: 4 residues within 4Å: Chain G: E.233, G.236, L.237, R.238 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:E.233 Water bridges: G:G.236 PEG.47: 5 residues within 4Å: Chain H: G.159, A.160, D.167, E.253, F.254 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:D.167 Water bridges: H:A.160, H:E.253, H:E.253

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

CL.24: 4 residues within 4Å: Chain D: L.204, S.205, P.216, D.217 Ligand excluded by PLIP CL.48: 4 residues within 4Å: Chain H: L.204, S.205, P.216, D.217 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

2021-07-28

Peptides

Enolase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

Enolase

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