SMTL ID : 5jio.1

Structure of Mycobacterium thermoresistibile trehalose-6-phosphate synthase ternary complex with ADP and Glucose-6-phosphate.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 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, N.389, L.390, V.391, E.394 Ligands: G6P.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.40, A:T.43, A:T.43, A:T.322, A:R.362, A:V.364, A:R.366, A:L.390, A:V.391, A:E.394 Water bridges: A:G.39, A:K.292, A:N.389, A:N.389 Salt bridges: A:R.287, A:K.292, A:K.292 ADP.5: 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: G6P.6 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:G.40, B:T.43, B:T.43, B:T.322, B:R.362, B:V.364, B:R.366, B:L.390, B:V.391, B:E.394 Water bridges: B:G.39, B:K.292, B:N.389, B:N.389 Salt bridges: B:R.287, B:K.292, B:K.292 ADP.9: 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: G6P.10 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:G.40, C:T.43, C:R.362, C:V.364, C:R.366, C:L.390, C:V.391, C:E.394 Water bridges: C:G.39, C:K.292, C:T.322, C:N.389, C:N.389 Salt bridges: C:R.287, C:K.292, C:K.292 ADP.13: 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: G6P.14 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:G.40, D:T.43, 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:T.322, D:N.389, D:N.389 Salt bridges: D:R.287, D:K.292, D:K.292

4 x G6P: 6-O-phosphono-alpha-D-glucopyranose(Non-covalent)

G6P.2: 14 residues within 4Å: Chain A: R.19, P.38, G.39, G.40, L.41, Y.91, D.145, Y.146, Q.147, H.169, I.170, R.287, R.325 Ligands: ADP.1 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.40, A:L.41, A:Y.91, A:D.145, A:Q.147 Water bridges: A:R.19, A:N.96, A:H.169, A:R.325 Salt bridges: A:R.19, A:R.287, A:R.325, A:R.325 G6P.6: 14 residues within 4Å: Chain B: R.19, P.38, G.39, G.40, L.41, Y.91, D.145, Y.146, Q.147, H.169, I.170, R.287, R.325 Ligands: ADP.5 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.40, B:L.41, B:Y.91, B:D.145, B:Q.147 Water bridges: B:R.19, B:N.96, B:H.169, B:R.325 Salt bridges: B:R.19, B:R.287, B:R.325, B:R.325 G6P.10: 14 residues within 4Å: Chain C: R.19, P.38, G.39, G.40, L.41, Y.91, D.145, Y.146, Q.147, H.169, I.170, R.287, R.325 Ligands: ADP.9 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:G.40, C:L.41, C:D.145, C:D.145, C:Q.147 Water bridges: C:R.19, C:Y.91, C:N.96, C:H.169, C:R.325 Salt bridges: C:R.19, C:R.287, C:R.325, C:R.325 G6P.14: 14 residues within 4Å: Chain D: R.19, P.38, G.39, G.40, L.41, Y.91, D.145, Y.146, Q.147, H.169, I.170, R.287, R.325 Ligands: ADP.13 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:G.40, D:L.41, D:D.145, D:D.145, D:Q.147 Water bridges: D:R.19, D:Y.91, D:N.96, D:H.169, D:R.325 Salt bridges: D:R.19, D:R.287, D:R.325, D:R.325

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

EDO.3: 3 residues within 4Å: Chain A: S.83, D.85, R.119 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.83, A:S.83, A:D.85, A:R.119, A:R.119 Water bridges: A:A.84 EDO.4: 3 residues within 4Å: Chain A: W.117, V.121, E.186 2 PLIP interactions: 2 interactions with chain A Water bridges: A:W.117, A:E.186 EDO.7: 3 residues within 4Å: Chain B: S.83, D.85, R.119 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.83, B:S.83, B:D.85, B:R.119, B:R.119 Water bridges: B:A.84 EDO.8: 3 residues within 4Å: Chain B: W.117, V.121, E.186 2 PLIP interactions: 2 interactions with chain B Water bridges: B:W.117, B:E.186 EDO.11: 3 residues within 4Å: Chain C: S.83, D.85, R.119 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.83, C:S.83, C:R.119, C:R.119 Water bridges: C:A.84 EDO.12: 3 residues within 4Å: Chain C: W.117, V.121, E.186 2 PLIP interactions: 2 interactions with chain C Water bridges: C:W.117, C:E.186 EDO.15: 3 residues within 4Å: Chain D: S.83, D.85, R.119 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.83, D:S.83, D:R.119, D:R.119 Water bridges: D:A.84 EDO.16: 3 residues within 4Å: Chain D: W.117, V.121, E.186 2 PLIP interactions: 2 interactions with chain D Water bridges: D:W.117, D:E.186

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

2017-05-10

Peptides

Alpha,alpha-trehalose-phosphate synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Alpha,alpha-trehalose-phosphate synthase

Related Entries With Identical Sequence