SMTL ID : 6ayv.1

Crystal structure of fructose-1,6-bisphosphatase T84A from Mycobacterium tuberculosis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x F6P: 6-O-phosphono-beta-D-fructofuranose(Non-covalent)

F6P.1: 13 residues within 4Å: Chain A: D.101, G.102, Y.133, L.176, R.178, R.180, D.200, G.201, D.202, G.223, G.224, E.227 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:D.101, A:Y.133, A:Y.133, A:K.136, A:R.178, A:D.200, A:D.200, A:G.201, A:D.202, A:D.202, A:D.202, A:G.224 Water bridges: A:G.102, A:G.102, A:A.103 Salt bridges: A:R.178, A:R.180 F6P.12: 12 residues within 4Å: Chain B: D.101, G.102, Y.133, R.178, R.180, D.200, G.201, D.202, G.223, G.224, E.227 Ligands: MG.14 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:D.101, B:Y.133, B:Y.133, B:R.178, B:G.201, B:D.202, B:D.202, B:G.224, B:E.227 Water bridges: B:I.100, B:G.102, B:G.102, B:A.103, B:D.200, B:E.227 Salt bridges: B:R.178, B:R.180 F6P.18: 13 residues within 4Å: Chain C: D.101, G.102, Y.133, L.176, R.178, R.180, D.200, G.201, D.202, G.223, G.224, E.227 Ligands: MG.19 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:D.101, C:Y.133, C:K.136, C:R.178, C:D.200, C:G.201, C:D.202, C:D.202, C:G.224, C:E.227 Water bridges: C:G.102, C:G.102, C:A.103 Salt bridges: C:R.178, C:R.180 F6P.29: 12 residues within 4Å: Chain D: D.101, G.102, Y.133, R.178, R.180, D.200, G.201, D.202, G.223, G.224, E.227 Ligands: MG.31 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:D.101, D:Y.133, D:R.178, D:D.200, D:G.201, D:D.202, D:D.202, D:D.202, D:G.224 Water bridges: D:I.100, D:G.102, D:G.102, D:A.103, D:D.200, D:E.227 Salt bridges: D:R.178, D:R.180

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.98, I.100, D.101, G.102, E.227 Ligands: F6P.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.98, A:D.101, A:E.227, H2O.4 MG.6: 7 residues within 4Å: Chain A: S.208, A.209, C.210, R.211, P.212, S.214, T.216 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.208, A:A.209, A:R.211, A:T.216, H2O.1 MG.14: 4 residues within 4Å: Chain B: D.98, D.101, E.227 Ligands: F6P.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.98, B:D.101, B:E.227, H2O.10 MG.19: 6 residues within 4Å: Chain C: D.98, I.100, D.101, G.102, E.227 Ligands: F6P.18 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.98, C:D.101, C:E.227, H2O.15 MG.23: 7 residues within 4Å: Chain C: S.208, A.209, C.210, R.211, P.212, S.214, T.216 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.208, C:A.209, C:R.211, C:T.216, H2O.13 MG.31: 4 residues within 4Å: Chain D: D.98, D.101, E.227 Ligands: F6P.29 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.98, D:D.101, D:E.227, H2O.22

22 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: P.91, D.121 Ligand excluded by PLIP GOL.4: 9 residues within 4Å: Chain A: N.135, K.136, I.149, A.151, I.153, N.156, L.184, A.220, G.221 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: R.310, S.313, T.315, R.317 Chain D: R.24, H.323 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: T.111, G.289, D.290 Chain B: T.111, N.112, G.289, D.290 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain A: M.110, T.111 Chain B: M.110, T.111, I.198, T.199 Ligand excluded by PLIP GOL.10: 9 residues within 4Å: Chain A: Y.322, R.324, S.332, A.333, I.334, F.336 Chain D: R.211, M.238, V.316 Ligand excluded by PLIP GOL.11: 7 residues within 4Å: Chain A: G.109, T.287, D.288, V.295, R.296 Chain B: R.196, G.215 Ligand excluded by PLIP GOL.13: 9 residues within 4Å: Chain B: N.135, K.136, I.149, A.151, P.152, I.153, N.156, L.184, G.221 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain B: R.310, S.313, T.315, R.317 Chain C: R.24, H.323 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain B: Y.80, G.82, E.83, E.84 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain B: V.67, I.68, G.69, G.71, N.81, P.226 Ligand excluded by PLIP GOL.20: 2 residues within 4Å: Chain C: P.91, D.121 Ligand excluded by PLIP GOL.21: 9 residues within 4Å: Chain C: N.135, K.136, I.149, A.151, I.153, N.156, L.184, A.220, G.221 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain B: R.24, H.323 Chain C: R.310, S.313, T.315, R.317 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain C: T.111, G.289, D.290 Chain D: T.111, N.112, G.289, D.290 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain C: M.110, T.111 Chain D: M.110, T.111, I.198, T.199 Ligand excluded by PLIP GOL.27: 9 residues within 4Å: Chain B: R.211, M.238, V.316 Chain C: Y.322, R.324, S.332, A.333, I.334, F.336 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain C: G.109, T.287, D.288, V.295, R.296 Chain D: R.196, G.215 Ligand excluded by PLIP GOL.30: 9 residues within 4Å: Chain D: N.135, K.136, I.149, A.151, P.152, I.153, N.156, L.184, G.221 Ligand excluded by PLIP GOL.32: 6 residues within 4Å: Chain A: R.24, H.323 Chain D: R.310, S.313, T.315, R.317 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain D: Y.80, G.82, E.83, E.84 Ligand excluded by PLIP GOL.34: 6 residues within 4Å: Chain D: V.67, I.68, G.69, G.71, N.81, P.226 Ligand excluded by PLIP

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.9: 10 residues within 4Å: Chain A: K.293, R.296, Y.298, T.303, H.305, E.320, D.335, F.336, T.337 Chain B: H.213 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.298, A:Y.298, A:Y.298, A:T.303, A:E.320, A:T.337 Water bridges: A:R.296 Salt bridges: A:K.293, A:K.293, A:R.296, A:H.305, B:H.213 MLI.26: 10 residues within 4Å: Chain C: K.293, R.296, Y.298, T.303, H.305, E.320, D.335, F.336, T.337 Chain D: H.213 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Y.298, C:Y.298, C:Y.298, C:T.337 Water bridges: C:R.296 Salt bridges: C:K.293, C:K.293, C:R.296, C:H.305, D:H.213

Links

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Citation

Wolf, N.M. et al., Structures of the Mycobacterium tuberculosis GlpX protein (class II fructose-1,6-bisphosphatase): implications for the active oligomeric state, catalytic mechanism and citrate inhibition. Acta Crystallogr D Struct Biol (2018)

Release Date

2018-03-14

Peptides

Fructose-1,6-bisphosphatase class 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Fructose-1,6-bisphosphatase class 2