SMTL ID : 7clk.1

Mycobacterium tuberculosis enolase in complex with alternate 2-phosphoglycerate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-octamer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: A.336, N.337, G.363, Y.364 Ligand excluded by PLIP EDO.2: 3 residues within 4Å: Chain A: Q.71 Chain E: V.182, E.183 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: A.84, I.86, L.88 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: R.186, W.187, E.190 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: L.281, G.282, A.283, Y.284, P.285 Ligands: ACT.12 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: A.178, P.179, Y.422, G.424, L.426 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: E.190, H.193, A.194 Chain E: Y.65, G.66 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: A.336, N.337, G.363, Y.364 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain B: Q.71 Chain F: V.182, E.183 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain B: A.84, I.86, L.88 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: R.186, W.187, E.190 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: L.281, G.282, A.283, Y.284, P.285 Ligands: ACT.27 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: A.178, P.179, Y.422, G.424, L.426 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain B: E.190, H.193, A.194 Chain F: Y.65, G.66 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain C: A.336, N.337, G.363, Y.364 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain C: Q.71 Chain H: V.182, E.183 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain C: A.84, I.86, L.88 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain C: R.186, W.187, E.190 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain C: L.281, G.282, A.283, Y.284, P.285 Ligands: ACT.42 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain C: A.178, P.179, Y.422, G.424, L.426 Ligand excluded by PLIP EDO.45: 5 residues within 4Å: Chain C: E.190, H.193, A.194 Chain H: Y.65, G.66 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain D: A.336, N.337, G.363, Y.364 Ligand excluded by PLIP EDO.47: 3 residues within 4Å: Chain D: Q.71 Chain G: V.182, E.183 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain D: A.84, I.86, L.88 Ligand excluded by PLIP EDO.49: 3 residues within 4Å: Chain D: R.186, W.187, E.190 Ligand excluded by PLIP EDO.50: 6 residues within 4Å: Chain D: L.281, G.282, A.283, Y.284, P.285 Ligands: ACT.57 Ligand excluded by PLIP EDO.51: 5 residues within 4Å: Chain D: A.178, P.179, Y.422, G.424, L.426 Ligand excluded by PLIP EDO.60: 5 residues within 4Å: Chain D: E.190, H.193, A.194 Chain G: Y.65, G.66 Ligand excluded by PLIP EDO.61: 4 residues within 4Å: Chain E: A.336, N.337, G.363, Y.364 Ligand excluded by PLIP EDO.62: 3 residues within 4Å: Chain A: V.182, E.183 Chain E: Q.71 Ligand excluded by PLIP EDO.63: 3 residues within 4Å: Chain E: A.84, I.86, L.88 Ligand excluded by PLIP EDO.64: 3 residues within 4Å: Chain E: R.186, W.187, E.190 Ligand excluded by PLIP EDO.65: 6 residues within 4Å: Chain E: L.281, G.282, A.283, Y.284, P.285 Ligands: ACT.72 Ligand excluded by PLIP EDO.66: 5 residues within 4Å: Chain E: A.178, P.179, Y.422, G.424, L.426 Ligand excluded by PLIP EDO.75: 5 residues within 4Å: Chain A: Y.65, G.66 Chain E: E.190, H.193, A.194 Ligand excluded by PLIP EDO.76: 4 residues within 4Å: Chain F: A.336, N.337, G.363, Y.364 Ligand excluded by PLIP EDO.77: 3 residues within 4Å: Chain B: V.182, E.183 Chain F: Q.71 Ligand excluded by PLIP EDO.78: 3 residues within 4Å: Chain F: A.84, I.86, L.88 Ligand excluded by PLIP EDO.79: 3 residues within 4Å: Chain F: R.186, W.187, E.190 Ligand excluded by PLIP EDO.80: 6 residues within 4Å: Chain F: L.281, G.282, A.283, Y.284, P.285 Ligands: ACT.87 Ligand excluded by PLIP EDO.81: 5 residues within 4Å: Chain F: A.178, P.179, Y.422, G.424, L.426 Ligand excluded by PLIP EDO.90: 5 residues within 4Å: Chain B: Y.65, G.66 Chain F: E.190, H.193, A.194 Ligand excluded by PLIP EDO.91: 4 residues within 4Å: Chain G: A.336, N.337, G.363, Y.364 Ligand excluded by PLIP EDO.92: 3 residues within 4Å: Chain D: V.182, E.183 Chain G: Q.71 Ligand excluded by PLIP EDO.93: 3 residues within 4Å: Chain G: A.84, I.86, L.88 Ligand excluded by PLIP EDO.94: 3 residues within 4Å: Chain G: R.186, W.187, E.190 Ligand excluded by PLIP EDO.95: 6 residues within 4Å: Chain G: L.281, G.282, A.283, Y.284, P.285 Ligands: ACT.102 Ligand excluded by PLIP EDO.96: 5 residues within 4Å: Chain G: A.178, P.179, Y.422, G.424, L.426 Ligand excluded by PLIP EDO.105: 5 residues within 4Å: Chain D: Y.65, G.66 Chain G: E.190, H.193, A.194 Ligand excluded by PLIP EDO.106: 4 residues within 4Å: Chain H: A.336, N.337, G.363, Y.364 Ligand excluded by PLIP EDO.107: 3 residues within 4Å: Chain C: V.182, E.183 Chain H: Q.71 Ligand excluded by PLIP EDO.108: 3 residues within 4Å: Chain H: A.84, I.86, L.88 Ligand excluded by PLIP EDO.109: 3 residues within 4Å: Chain H: R.186, W.187, E.190 Ligand excluded by PLIP EDO.110: 6 residues within 4Å: Chain H: L.281, G.282, A.283, Y.284, P.285 Ligands: ACT.117 Ligand excluded by PLIP EDO.111: 5 residues within 4Å: Chain H: A.178, P.179, Y.422, G.424, L.426 Ligand excluded by PLIP EDO.120: 5 residues within 4Å: Chain C: Y.65, G.66 Chain H: E.190, H.193, A.194 Ligand excluded by PLIP

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

ACT.7: 8 residues within 4Å: Chain A: I.19, E.29, R.41, A.42, A.43, E.376, D.377 Chain E: R.411 Ligand excluded by PLIP ACT.8: 5 residues within 4Å: Chain A: F.255, D.257, G.258, D.296, D.297 Ligand excluded by PLIP ACT.9: 1 residues within 4Å: Chain A: D.354 Ligand excluded by PLIP ACT.10: 6 residues within 4Å: Chain A: I.10, I.11, E.12, I.35, I.86, G.87 Ligand excluded by PLIP ACT.11: 3 residues within 4Å: Chain A: F.137, Q.408, A.415 Ligand excluded by PLIP ACT.12: 4 residues within 4Å: Chain A: G.240, P.285, V.287 Ligands: EDO.5 Ligand excluded by PLIP ACT.22: 8 residues within 4Å: Chain B: I.19, E.29, R.41, A.42, A.43, E.376, D.377 Chain F: R.411 Ligand excluded by PLIP ACT.23: 5 residues within 4Å: Chain B: F.255, D.257, G.258, D.296, D.297 Ligand excluded by PLIP ACT.24: 1 residues within 4Å: Chain B: D.354 Ligand excluded by PLIP ACT.25: 6 residues within 4Å: Chain B: I.10, I.11, E.12, I.35, I.86, G.87 Ligand excluded by PLIP ACT.26: 3 residues within 4Å: Chain B: F.137, Q.408, A.415 Ligand excluded by PLIP ACT.27: 4 residues within 4Å: Chain B: G.240, P.285, V.287 Ligands: EDO.20 Ligand excluded by PLIP ACT.37: 8 residues within 4Å: Chain C: I.19, E.29, R.41, A.42, A.43, E.376, D.377 Chain H: R.411 Ligand excluded by PLIP ACT.38: 5 residues within 4Å: Chain C: F.255, D.257, G.258, D.296, D.297 Ligand excluded by PLIP ACT.39: 1 residues within 4Å: Chain C: D.354 Ligand excluded by PLIP ACT.40: 6 residues within 4Å: Chain C: I.10, I.11, E.12, I.35, I.86, G.87 Ligand excluded by PLIP ACT.41: 3 residues within 4Å: Chain C: F.137, Q.408, A.415 Ligand excluded by PLIP ACT.42: 4 residues within 4Å: Chain C: G.240, P.285, V.287 Ligands: EDO.35 Ligand excluded by PLIP ACT.52: 8 residues within 4Å: Chain D: I.19, E.29, R.41, A.42, A.43, E.376, D.377 Chain G: R.411 Ligand excluded by PLIP ACT.53: 5 residues within 4Å: Chain D: F.255, D.257, G.258, D.296, D.297 Ligand excluded by PLIP ACT.54: 1 residues within 4Å: Chain D: D.354 Ligand excluded by PLIP ACT.55: 6 residues within 4Å: Chain D: I.10, I.11, E.12, I.35, I.86, G.87 Ligand excluded by PLIP ACT.56: 3 residues within 4Å: Chain D: F.137, Q.408, A.415 Ligand excluded by PLIP ACT.57: 4 residues within 4Å: Chain D: G.240, P.285, V.287 Ligands: EDO.50 Ligand excluded by PLIP ACT.67: 8 residues within 4Å: Chain A: R.411 Chain E: I.19, E.29, R.41, A.42, A.43, E.376, D.377 Ligand excluded by PLIP ACT.68: 5 residues within 4Å: Chain E: F.255, D.257, G.258, D.296, D.297 Ligand excluded by PLIP ACT.69: 1 residues within 4Å: Chain E: D.354 Ligand excluded by PLIP ACT.70: 6 residues within 4Å: Chain E: I.10, I.11, E.12, I.35, I.86, G.87 Ligand excluded by PLIP ACT.71: 3 residues within 4Å: Chain E: F.137, Q.408, A.415 Ligand excluded by PLIP ACT.72: 4 residues within 4Å: Chain E: G.240, P.285, V.287 Ligands: EDO.65 Ligand excluded by PLIP ACT.82: 8 residues within 4Å: Chain B: R.411 Chain F: I.19, E.29, R.41, A.42, A.43, E.376, D.377 Ligand excluded by PLIP ACT.83: 5 residues within 4Å: Chain F: F.255, D.257, G.258, D.296, D.297 Ligand excluded by PLIP ACT.84: 1 residues within 4Å: Chain F: D.354 Ligand excluded by PLIP ACT.85: 6 residues within 4Å: Chain F: I.10, I.11, E.12, I.35, I.86, G.87 Ligand excluded by PLIP ACT.86: 3 residues within 4Å: Chain F: F.137, Q.408, A.415 Ligand excluded by PLIP ACT.87: 4 residues within 4Å: Chain F: G.240, P.285, V.287 Ligands: EDO.80 Ligand excluded by PLIP ACT.97: 8 residues within 4Å: Chain D: R.411 Chain G: I.19, E.29, R.41, A.42, A.43, E.376, D.377 Ligand excluded by PLIP ACT.98: 5 residues within 4Å: Chain G: F.255, D.257, G.258, D.296, D.297 Ligand excluded by PLIP ACT.99: 1 residues within 4Å: Chain G: D.354 Ligand excluded by PLIP ACT.100: 6 residues within 4Å: Chain G: I.10, I.11, E.12, I.35, I.86, G.87 Ligand excluded by PLIP ACT.101: 3 residues within 4Å: Chain G: F.137, Q.408, A.415 Ligand excluded by PLIP ACT.102: 4 residues within 4Å: Chain G: G.240, P.285, V.287 Ligands: EDO.95 Ligand excluded by PLIP ACT.112: 8 residues within 4Å: Chain C: R.411 Chain H: I.19, E.29, R.41, A.42, A.43, E.376, D.377 Ligand excluded by PLIP ACT.113: 5 residues within 4Å: Chain H: F.255, D.257, G.258, D.296, D.297 Ligand excluded by PLIP ACT.114: 1 residues within 4Å: Chain H: D.354 Ligand excluded by PLIP ACT.115: 6 residues within 4Å: Chain H: I.10, I.11, E.12, I.35, I.86, G.87 Ligand excluded by PLIP ACT.116: 3 residues within 4Å: Chain H: F.137, Q.408, A.415 Ligand excluded by PLIP ACT.117: 4 residues within 4Å: Chain H: G.240, P.285, V.287 Ligands: EDO.110 Ligand excluded by PLIP

8 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 7 residues within 4Å: Chain A: Q.169, D.248, E.290, D.317, K.342, K.393 Ligands: 2PG.14 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.248, A:E.290, A:D.317, H2O.3, H2O.4 MG.28: 7 residues within 4Å: Chain B: Q.169, D.248, E.290, D.317, K.342, K.393 Ligands: 2PG.29 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.248, B:E.290, B:D.317, H2O.9, H2O.11 MG.43: 7 residues within 4Å: Chain C: Q.169, D.248, E.290, D.317, K.342, K.393 Ligands: 2PG.44 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.248, C:E.290, C:D.317, H2O.16, H2O.18 MG.58: 7 residues within 4Å: Chain D: Q.169, D.248, E.290, D.317, K.342, K.393 Ligands: 2PG.59 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.248, D:E.290, D:D.317, H2O.23, H2O.25 MG.73: 7 residues within 4Å: Chain E: Q.169, D.248, E.290, D.317, K.342, K.393 Ligands: 2PG.74 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.248, E:E.290, E:D.317, H2O.30, H2O.31 MG.88: 7 residues within 4Å: Chain F: Q.169, D.248, E.290, D.317, K.342, K.393 Ligands: 2PG.89 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.248, F:E.290, F:D.317, H2O.36, H2O.38 MG.103: 7 residues within 4Å: Chain G: Q.169, D.248, E.290, D.317, K.342, K.393 Ligands: 2PG.104 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.248, G:E.290, G:D.317, H2O.43, H2O.45 MG.118: 7 residues within 4Å: Chain H: Q.169, D.248, E.290, D.317, K.342, K.393 Ligands: 2PG.119 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.248, H:E.290, H:D.317, H2O.50, H2O.52

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

2PG.14: 17 residues within 4Å: Chain A: G.47, A.48, S.49, T.50, E.54, H.161, Q.169, E.170, D.248, A.250, D.317, D.318, K.342, Q.345, R.371, S.372 Ligands: MG.13 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:A.48, A:S.49, A:S.49, A:S.49, A:Q.169, A:E.170, A:D.318, A:K.342, A:Q.345, A:S.372 Water bridges: A:E.211, A:E.290, A:D.291, A:D.291, A:K.393 Salt bridges: A:H.161, A:K.342, A:K.342, A:R.371 2PG.29: 17 residues within 4Å: Chain B: G.47, A.48, S.49, T.50, E.54, H.161, Q.169, E.170, D.248, A.250, D.317, D.318, K.342, Q.345, R.371, S.372 Ligands: MG.28 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:A.48, B:S.49, B:S.49, B:S.49, B:Q.169, B:E.170, B:D.318, B:K.342, B:Q.345, B:S.372 Water bridges: B:E.211, B:E.290, B:D.291, B:D.291, B:K.393 Salt bridges: B:H.161, B:K.342, B:K.342, B:R.371 2PG.44: 17 residues within 4Å: Chain C: G.47, A.48, S.49, T.50, E.54, H.161, Q.169, E.170, D.248, A.250, D.317, D.318, K.342, Q.345, R.371, S.372 Ligands: MG.43 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:A.48, C:S.49, C:S.49, C:S.49, C:Q.169, C:E.170, C:D.318, C:K.342, C:Q.345, C:S.372 Water bridges: C:E.211, C:E.290, C:D.291, C:D.291, C:K.393 Salt bridges: C:H.161, C:K.342, C:K.342, C:R.371 2PG.59: 17 residues within 4Å: Chain D: G.47, A.48, S.49, T.50, E.54, H.161, Q.169, E.170, D.248, A.250, D.317, D.318, K.342, Q.345, R.371, S.372 Ligands: MG.58 19 PLIP interactions: 19 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:D.318, D:K.342, D:Q.345, D:S.372 Water bridges: D:E.211, D:E.290, D:D.291, D:D.291, D:K.393 Salt bridges: D:H.161, D:K.342, D:K.342, D:R.371 2PG.74: 17 residues within 4Å: Chain E: G.47, A.48, S.49, T.50, E.54, H.161, Q.169, E.170, D.248, A.250, D.317, D.318, K.342, Q.345, R.371, S.372 Ligands: MG.73 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:A.48, E:S.49, E:S.49, E:S.49, E:Q.169, E:D.318, E:K.342, E:Q.345, E:R.371, E:S.372 Water bridges: E:E.211, E:D.318, E:K.393 Salt bridges: E:H.161, E:K.342, E:K.342, E:R.371 2PG.89: 17 residues within 4Å: Chain F: G.47, A.48, S.49, T.50, E.54, H.161, Q.169, E.170, D.248, A.250, D.317, D.318, K.342, Q.345, R.371, S.372 Ligands: MG.88 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:A.48, F:S.49, F:S.49, F:S.49, F:Q.169, F:D.318, F:K.342, F:Q.345, F:R.371, F:S.372 Water bridges: F:E.211, F:D.318, F:K.393 Salt bridges: F:H.161, F:K.342, F:K.342, F:R.371 2PG.104: 17 residues within 4Å: Chain G: G.47, A.48, S.49, T.50, E.54, H.161, Q.169, E.170, D.248, A.250, D.317, D.318, K.342, Q.345, R.371, S.372 Ligands: MG.103 17 PLIP interactions: 17 interactions with chain G Hydrogen bonds: G:A.48, G:S.49, G:S.49, G:S.49, G:Q.169, G:D.318, G:K.342, G:Q.345, G:R.371, G:S.372 Water bridges: G:E.211, G:D.318, G:K.393 Salt bridges: G:H.161, G:K.342, G:K.342, G:R.371 2PG.119: 17 residues within 4Å: Chain H: G.47, A.48, S.49, T.50, E.54, H.161, Q.169, E.170, D.248, A.250, D.317, D.318, K.342, Q.345, R.371, S.372 Ligands: MG.118 19 PLIP interactions: 19 interactions with chain H Hydrogen bonds: H:A.48, H:S.49, H:S.49, H:S.49, H:Q.169, H:D.318, H:K.342, H:Q.345, H:R.371, H:S.372 Water bridges: H:E.211, H:D.317, H:D.317, H:D.318, H:K.393 Salt bridges: H:H.161, H:K.342, H:K.342, H:R.371

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

2022-01-26

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

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