SMTL ID : 3ekl.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 Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

homo-tetramer

Ligands

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

13P.1: 17 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, ZN.3, NA.5 10 PLIP interactions: 1 interactions with chain B, 9 interactions with chain A Water bridges: B:K.308 Hydrogen bonds: A:G.213, A:G.253, A:G.254, A:S.255, A:S.255, A:D.276, A:D.276, A:D.276, A:T.277 13P.2: 18 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, ZN.3, NA.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.51, A:G.213, A:G.253, A:G.254, A:S.255, A:D.276, A:T.277 Water bridges: A:D.276, A:D.276 13P.6: 17 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.7, ZN.8, NA.10 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.213, B:G.253, B:G.254, B:S.255, B:S.255, B:D.276, B:D.276, B:D.276, B:T.277 Water bridges: A:K.308 13P.7: 18 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.6, ZN.8, NA.10 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.51, B:G.213, B:G.253, B:G.254, B:S.255, B:D.276, B:T.277 Water bridges: B:D.276, B:D.276 13P.11: 17 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.12, ZN.13, NA.15 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.213, C:G.253, C:G.254, C:S.255, C:S.255, C:D.276, C:D.276, C:T.277, C:T.277 Water bridges: D:K.308 13P.12: 18 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.11, ZN.13, NA.15 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:Q.51, C:G.213, C:G.253, C:G.254, C:S.255, C:D.276, C:T.277, C:T.277 13P.16: 17 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.17, ZN.18, NA.20 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.213, D:G.253, D:G.254, D:S.255, D:S.255, D:D.276, D:D.276, D:T.277, D:T.277 Water bridges: C:K.308 13P.17: 18 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.16, ZN.18, NA.20 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Q.51, D:G.213, D:G.253, D:G.254, D:S.255, D:D.276, D:T.277, D:T.277

8 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: H.96, H.212, H.252, N.274 Ligands: 13P.1, 13P.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.96, A:H.212, A:H.252 ZN.4: 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.5 ZN.8: 6 residues within 4Å: Chain B: H.96, H.212, H.252, N.274 Ligands: 13P.6, 13P.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.96, B:H.212, B:H.252 ZN.9: 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.24 ZN.13: 6 residues within 4Å: Chain C: H.96, H.212, H.252, N.274 Ligands: 13P.11, 13P.12 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.96, C:H.212, C:H.252 ZN.14: 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.43 ZN.18: 6 residues within 4Å: Chain D: H.96, H.212, H.252, N.274 Ligands: 13P.16, 13P.17 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.96, D:H.212, D:H.252 ZN.19: 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.63

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

NA.5: 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.6, 13P.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.213, B:G.213 Water bridges: B:V.211 NA.15: 6 residues within 4Å: Chain C: V.211, G.213, G.253, S.255 Ligands: 13P.11, 13P.12 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.213, C:S.255 Water bridges: C:V.211 NA.20: 6 residues within 4Å: Chain D: V.211, G.213, G.253, S.255 Ligands: 13P.16, 13P.17 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.211, D:G.213 Water bridges: D:V.211

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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