SMTL ID : 3ekz.1

Structural Characterization of tetrameric Mycobacterium tuberculosis fructose 1,6-bisphosphate aldolase - substrate binding and catalysis mechanism of a class IIa bacterial aldolase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-tetramer

Ligands

8 x 13P: 1,3-DIHYDROXYACETONEPHOSPHATE(Non-covalent)

13P.1: 18 residues within 4Å: Chain A: N.27, Q.51, D.95, V.211, H.212, G.213, H.252, G.253, G.254, S.255, N.274, V.275, D.276, T.277 Ligands: 13P.2, G3P.3, NA.4, ZN.5 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.27, A:Q.51, A:G.213, A:G.253, A:G.254, A:S.255, A:D.276, A:T.277 Water bridges: B:K.308 13P.2: 19 residues within 4Å: Chain A: N.27, Q.51, D.95, H.96, V.211, H.212, G.213, H.252, G.253, G.254, S.255, N.274, V.275, D.276, T.277 Ligands: 13P.1, G3P.3, NA.4, ZN.5 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.51, A:G.213, A:G.253, A:S.255, A:S.255, A:D.276, A:T.277 Water bridges: B:K.308 13P.7: 18 residues within 4Å: Chain B: N.27, Q.51, D.95, V.211, H.212, G.213, H.252, G.253, G.254, S.255, N.274, V.275, D.276, T.277 Ligands: 13P.8, G3P.9, NA.10, ZN.11 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.27, B:Q.51, B:G.213, B:G.253, B:G.254, B:S.255, B:D.276, B:T.277 Water bridges: A:K.308 13P.8: 19 residues within 4Å: Chain B: N.27, Q.51, D.95, H.96, V.211, H.212, G.213, H.252, G.253, G.254, S.255, N.274, V.275, D.276, T.277 Ligands: 13P.7, G3P.9, NA.10, ZN.11 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.51, B:G.213, B:G.253, B:S.255, B:S.255, B:D.276, B:T.277 Water bridges: A:K.308 13P.13: 18 residues within 4Å: Chain C: N.27, Q.51, D.95, V.211, H.212, G.213, H.252, G.253, G.254, S.255, N.274, V.275, D.276, T.277 Ligands: 13P.14, G3P.15, NA.16, ZN.17 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:N.27, C:Q.51, C:G.213, C:H.252, C:G.253, C:G.254, C:S.255, C:D.276, C:T.277, C:T.277 Water bridges: D:K.308 13P.14: 19 residues within 4Å: Chain C: N.27, Q.51, D.95, H.96, V.211, H.212, G.213, H.252, G.253, G.254, S.255, N.274, V.275, D.276, T.277 Ligands: 13P.13, G3P.15, NA.16, ZN.17 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Q.51, C:G.213, C:H.252, C:G.253, C:S.255, C:S.255, C:D.276, C:T.277, C:T.277 Water bridges: D:K.308 13P.19: 18 residues within 4Å: Chain D: N.27, Q.51, D.95, V.211, H.212, G.213, H.252, G.253, G.254, S.255, N.274, V.275, D.276, T.277 Ligands: 13P.20, G3P.21, NA.22, ZN.23 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:N.27, D:Q.51, D:G.213, D:G.253, D:G.254, D:S.255, D:D.276, D:T.277, D:T.277 Water bridges: C:K.308 13P.20: 19 residues within 4Å: Chain D: N.27, Q.51, D.95, H.96, V.211, H.212, G.213, H.252, G.253, G.254, S.255, N.274, V.275, D.276, T.277 Ligands: 13P.19, G3P.21, NA.22, ZN.23 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.51, D:G.213, D:G.253, D:S.255, D:S.255, D:D.276, D:T.277, D:T.277 Water bridges: C:K.308

4 x G3P: SN-GLYCEROL-3-PHOSPHATE(Non-covalent)

G3P.3: 11 residues within 4Å: Chain A: N.27, S.53, G.56, D.95, H.96, H.212, D.276 Chain B: R.314 Ligands: 13P.1, 13P.2, ZN.5 13 PLIP interactions: 5 interactions with chain B, 8 interactions with chain A Water bridges: B:K.308, B:K.308, B:R.314, B:R.314, A:N.27, A:N.27, A:G.55 Salt bridges: B:R.314 Hydrogen bonds: A:S.53, A:S.53, A:G.56, A:H.212, A:D.276 G3P.9: 11 residues within 4Å: Chain A: R.314 Chain B: N.27, S.53, G.56, D.95, H.96, H.212, D.276 Ligands: 13P.7, 13P.8, ZN.11 13 PLIP interactions: 5 interactions with chain A, 8 interactions with chain B Water bridges: A:K.308, A:K.308, A:R.314, A:R.314, B:N.27, B:N.27, B:G.55 Salt bridges: A:R.314 Hydrogen bonds: B:S.53, B:S.53, B:G.56, B:H.212, B:D.276 G3P.15: 11 residues within 4Å: Chain C: N.27, S.53, G.56, D.95, H.96, H.212, D.276 Chain D: R.314 Ligands: 13P.13, 13P.14, ZN.17 12 PLIP interactions: 5 interactions with chain D, 7 interactions with chain C Water bridges: D:K.308, D:K.308, D:R.314, D:R.314, C:N.27, C:N.27, C:G.55 Salt bridges: D:R.314 Hydrogen bonds: C:S.53, C:S.53, C:G.56, C:H.212 G3P.21: 11 residues within 4Å: Chain C: R.314 Chain D: N.27, S.53, G.56, D.95, H.96, H.212, D.276 Ligands: 13P.19, 13P.20, ZN.23 12 PLIP interactions: 5 interactions with chain C, 7 interactions with chain D Water bridges: C:K.308, C:K.308, C:R.314, C:R.314, D:N.27, D:N.27, D:G.55 Salt bridges: C:R.314 Hydrogen bonds: D:S.53, D:S.53, D:G.56, D:H.212

4 x NA: SODIUM ION(Non-functional Binders)

NA.4: 6 residues within 4Å: Chain A: V.211, G.213, G.253, S.255 Ligands: 13P.1, 13P.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.211, A:G.213 Water bridges: A:V.211 NA.10: 6 residues within 4Å: Chain B: V.211, G.213, G.253, S.255 Ligands: 13P.7, 13P.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.213, B:S.255 Water bridges: B:V.211 NA.16: 6 residues within 4Å: Chain C: V.211, G.213, G.253, S.255 Ligands: 13P.13, 13P.14 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.213, C:S.255 Water bridges: C:V.211 NA.22: 6 residues within 4Å: Chain D: V.211, G.213, G.253, S.255 Ligands: 13P.19, 13P.20 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.211, D:G.213 Water bridges: D:V.211

8 x ZN: ZINC ION(Non-covalent)

ZN.5: 6 residues within 4Å: Chain A: H.96, H.212, H.252 Ligands: 13P.1, 13P.2, G3P.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.96, A:H.212, A:H.252 ZN.6: 2 residues within 4Å: Chain A: H.344, H.346 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.344, A:H.346, H2O.4 ZN.11: 6 residues within 4Å: Chain B: H.96, H.212, H.252 Ligands: 13P.7, 13P.8, G3P.9 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.96, B:H.212, B:H.252 ZN.12: 2 residues within 4Å: Chain B: H.344, H.346 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.344, B:H.346, H2O.18 ZN.17: 6 residues within 4Å: Chain C: H.96, H.212, H.252 Ligands: 13P.13, 13P.14, G3P.15 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.96, C:H.212, C:H.252 ZN.18: 2 residues within 4Å: Chain C: H.344, H.346 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.344, C:H.346, H2O.32 ZN.23: 6 residues within 4Å: Chain D: H.96, H.212, H.252 Ligands: 13P.19, 13P.20, G3P.21 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.96, D:H.212, D:H.252 ZN.24: 2 residues within 4Å: Chain D: H.344, H.346 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.344, D:H.346, H2O.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pegan, S.D. et al., Structural basis for catalysis of a tetrameric class IIa fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis. J.Mol.Biol. (2009)

Release Date

2009-02-10

Peptides

Fructose-bisphosphate aldolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Fructose-bisphosphate aldolase

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