SMTL ID : 5l3k.1 (1 other biounit)

Structure of Mycobacterium thermoresistibile trehalose-6-phosphate synthase in a ternary complex with ADP and fructose-6-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-tetramer

Ligands

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 20 residues within 4Å: Chain A: G.39, G.40, T.43, V.285, D.286, R.287, K.292, L.320, A.321, T.322, R.362, P.363, V.364, R.366, L.369, M.388, N.389, L.390, V.391, E.394 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.40, A:T.43, A:T.43, A:L.320, A:V.364, A:R.366, A:R.366, A:M.388, A:L.390, A:V.391, A:E.394 Water bridges: A:G.39, A:K.292, A:T.322, A:N.389 Salt bridges: A:R.287, A:K.292, A:K.292 ADP.3: 20 residues within 4Å: Chain B: G.39, G.40, T.43, V.285, D.286, R.287, K.292, L.320, A.321, T.322, R.362, P.363, V.364, R.366, L.369, N.389, L.390, V.391, E.394 Ligands: F6P.4 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:G.39, B:G.40, B:T.43, B:T.43, B:D.286, B:T.322, B:V.364, B:R.366, B:L.390, B:V.391, B:E.394 Water bridges: B:K.292, B:K.292, B:D.386, B:N.389 Salt bridges: B:R.287, B:K.292, B:K.292 ADP.6: 20 residues within 4Å: Chain C: G.39, G.40, T.43, V.285, D.286, R.287, K.292, L.320, A.321, T.322, R.362, P.363, V.364, R.366, L.369, N.389, L.390, V.391, E.394 Ligands: F6P.7 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:G.39, C:G.40, C:L.41, C:T.43, C:L.320, C:T.322, C:V.364, C:R.366, C:R.366, C:L.390, C:V.391, C:E.394 Water bridges: C:N.389 Salt bridges: C:R.287, C:K.292, C:K.292 ADP.9: 20 residues within 4Å: Chain D: G.39, G.40, T.43, V.285, D.286, R.287, K.292, L.320, A.321, T.322, R.362, P.363, V.364, R.366, L.369, N.389, L.390, V.391, E.394 Ligands: F6P.10 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:G.40, D:T.43, D:T.322, D:R.362, D:V.364, D:R.366, D:L.390, D:V.391, D:E.394 Water bridges: D:G.39, D:K.292, D:K.292, D:N.389 Salt bridges: D:R.287, D:K.292, D:K.292

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

EDO.2: 4 residues within 4Å: Chain A: R.312, E.313, E.351, H.354 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.312, A:E.351 EDO.8: 4 residues within 4Å: Chain B: Q.180 Chain C: I.107, L.384, H.427 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Q.180, C:L.384 Water bridges: B:Q.180, C:D.105

3 x F6P: 6-O-phosphono-beta-D-fructofuranose(Non-covalent)(Post Translational Modification)

F6P.4: 12 residues within 4Å: Chain B: R.19, G.39, Y.91, W.100, D.145, Y.146, Q.147, H.169, I.170, R.287, R.325 Ligands: ADP.3 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Y.91, B:D.145, B:Y.146, B:Y.146, B:Q.147, B:R.325 Water bridges: B:R.19, B:L.41, B:N.96, B:S.324 Salt bridges: B:R.19, B:R.325 F6P.7: 13 residues within 4Å: Chain C: R.19, P.38, L.41, Y.91, W.100, D.145, Y.146, Q.147, H.169, I.170, R.287, R.325 Ligands: ADP.6 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:D.145, C:Q.147 Water bridges: C:N.18, C:N.18, C:H.169, C:R.325, C:R.325 Salt bridges: C:R.19, C:R.325 F6P.10: 14 residues within 4Å: Chain D: R.19, P.38, G.39, L.41, Y.91, W.100, D.145, Y.146, Q.147, H.169, I.170, R.287, R.325 Ligands: ADP.9 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:Y.91, D:D.145, D:D.145, D:D.145, D:Q.147, D:R.287, D:R.325 Water bridges: D:Y.91, D:N.96, D:H.169, D:S.324 Salt bridges: D:R.19, D:R.325

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 1 residues within 4Å: Chain B: H.461 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.228 Salt bridges: B:H.461 PO4.11: 2 residues within 4Å: Chain D: R.228, H.461 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.228 Water bridges: D:H.461 Salt bridges: D:H.461 PO4.12: 4 residues within 4Å: Chain D: S.83, D.85, D.86, R.119 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.83, D:D.85, D:D.85 Water bridges: D:D.85 Salt bridges: D:R.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mendes, V. et al., Mycobacterial OtsA Structures Unveil Substrate Preference Mechanism and Allosteric Regulation by 2-Oxoglutarate and 2-Phosphoglycerate. Mbio (2019)

Release Date

2017-06-07

Peptides

Alpha,alpha-trehalose-phosphate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Alpha,alpha-trehalose-phosphate synthase

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