SMTL ID : 6ayu.1

Crystal structure of fructose-1,6-bisphosphatase T84S from Mycobacterium tuberculosis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

F6P.1: 15 residues within 4Å: Chain A: D.101, G.102, Y.133, K.136, L.176, R.178, R.180, D.200, G.201, D.202, G.223, G.224, E.227 Ligands: MG.2, GOL.7 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:D.101, A:G.102, A:Y.133, A:Y.133, A:K.136, A:R.178, A:D.200, A:G.201, A:D.202, A:D.202, A:D.202, A:G.224 Salt bridges: A:R.178, A:R.180 F6P.8: 13 residues within 4Å: Chain B: D.101, G.102, Y.133, K.136, R.178, R.180, D.200, G.201, D.202, G.223, G.224, E.227 Ligands: MG.10 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:D.101, B:Y.133, B:Y.133, B:K.136, B:R.178, B:G.201, B:D.202, B:D.202, B:G.224 Water bridges: B:D.200 Salt bridges: B:R.178, B:R.180 F6P.14: 15 residues within 4Å: Chain C: D.101, G.102, Y.133, K.136, L.176, R.178, R.180, D.200, G.201, D.202, G.223, G.224, E.227 Ligands: MG.15, GOL.20 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:D.101, C:G.102, C:Y.133, C:K.136, C:R.178, C:G.201, C:D.202, C:D.202, C:G.224, C:E.227 Salt bridges: C:R.178, C:R.180 F6P.21: 13 residues within 4Å: Chain D: D.101, G.102, Y.133, K.136, R.178, R.180, D.200, G.201, D.202, G.223, G.224, E.227 Ligands: MG.23 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:D.101, D:Y.133, D:K.136, D:R.178, D:D.200, D:G.201, D:D.202, D:D.202, D:D.202, D:G.224 Water bridges: D:D.200 Salt bridges: D:R.178, D:R.180

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: D.98, I.100, D.101, G.102, E.227 Ligands: F6P.1, GOL.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.98, A:D.101, A:E.227 MG.6: 6 residues within 4Å: Chain A: S.208, A.209, R.211, P.212, S.214, T.216 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:S.208, A:A.209, A:R.211, A:S.214, A:T.216 MG.10: 4 residues within 4Å: Chain B: D.98, D.101, E.227 Ligands: F6P.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.98, B:D.101, B:E.227 MG.15: 7 residues within 4Å: Chain C: D.98, I.100, D.101, G.102, E.227 Ligands: F6P.14, GOL.20 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.98, C:D.101, C:E.227 MG.19: 6 residues within 4Å: Chain C: S.208, A.209, R.211, P.212, S.214, T.216 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:S.208, C:A.209, C:R.211, C:S.214, C:T.216 MG.23: 4 residues within 4Å: Chain D: D.98, D.101, E.227 Ligands: F6P.21 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.98, D:D.101, D:E.227

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

MLI.3: 9 residues within 4Å: Chain A: R.296, Y.298, T.303, H.305, E.320, D.335, F.336, T.337 Chain B: H.213 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.298, A:Y.298, A:T.303, A:E.320, A:E.320 Salt bridges: A:H.305 MLI.16: 9 residues within 4Å: Chain C: R.296, Y.298, T.303, H.305, E.320, D.335, F.336, T.337 Chain D: H.213 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.298, C:Y.298, C:E.320, C:T.337 Salt bridges: C:H.305

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: N.135, K.136, I.149, A.151, I.153, N.156, G.221 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.135, A:K.136, A:I.149, A:N.156, A:G.221 Water bridges: A:N.135 GOL.5: 5 residues within 4Å: Chain A: S.313, T.315, R.317 Chain D: R.24, H.323 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:R.24, D:R.24, D:H.323, A:T.315, A:R.317 GOL.7: 7 residues within 4Å: Chain A: D.46, D.98, P.99, I.100, S.103 Ligands: F6P.1, MG.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.100, A:G.102, A:S.103 Water bridges: A:D.200 GOL.9: 9 residues within 4Å: Chain B: N.135, K.136, I.149, A.151, P.152, I.153, N.156, A.220, G.221 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.135, B:K.136, B:P.152, B:N.156, B:G.221 Water bridges: B:I.153, B:I.153 GOL.11: 5 residues within 4Å: Chain B: R.310, S.313, T.315, R.317 Chain C: R.24 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:R.310, B:R.310, B:S.313, B:T.315, B:R.317, C:R.24 Water bridges: C:H.323 GOL.12: 8 residues within 4Å: Chain B: V.67, I.68, G.69, G.71, N.81, P.128, S.129, P.226 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.69, B:G.69, B:G.71, B:N.81, B:S.129 GOL.13: 6 residues within 4Å: Chain A: M.110, T.111 Chain B: M.110, T.111, I.198, T.199 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:T.111, B:T.199, B:T.199, A:T.111, A:T.111, A:T.111 Water bridges: B:G.109, A:L.197 GOL.17: 7 residues within 4Å: Chain C: N.135, K.136, I.149, A.151, I.153, N.156, G.221 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.135, C:K.136, C:I.149, C:N.156, C:G.221 Water bridges: C:N.135 GOL.18: 5 residues within 4Å: Chain B: R.24, H.323 Chain C: S.313, T.315, R.317 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.24, B:R.24, B:H.323, C:R.317 GOL.20: 7 residues within 4Å: Chain C: D.46, D.98, P.99, I.100, S.103 Ligands: F6P.14, MG.15 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:I.100, C:G.102, C:S.103 Water bridges: C:D.200 GOL.22: 9 residues within 4Å: Chain D: N.135, K.136, I.149, A.151, P.152, I.153, N.156, A.220, G.221 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.135, D:K.136, D:P.152, D:N.156, D:G.221 Water bridges: D:I.153, D:I.153 GOL.24: 5 residues within 4Å: Chain A: R.24 Chain D: R.310, S.313, T.315, R.317 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:R.24, D:R.310, D:R.310, D:S.313, D:R.317 Water bridges: A:H.323 GOL.25: 8 residues within 4Å: Chain D: V.67, I.68, G.69, G.71, N.81, P.128, S.129, P.226 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:G.69, D:G.69, D:G.71, D:N.81, D:S.129 GOL.26: 6 residues within 4Å: Chain C: M.110, T.111 Chain D: M.110, T.111, I.198, T.199 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:T.111, C:T.111, D:T.111, D:T.199, D:T.199 Water bridges: C:L.197, D:G.109

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