SMTL ID : 5k5c.1

Structure of Mycobacterium thermoresistibile trehalose-6-phosphate synthase in a complex with Trehalose.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x GLC- GLC: alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 15 residues within 4Å: Chain A: W.100, Y.146, H.169, I.170, H.200, I.248, R.287, R.325, D.386, G.387, M.388, N.389, L.390 Ligands: NHE.3, EDO.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.386, A:G.387, A:M.388, A:N.389, A:L.390 Water bridges: A:K.292, A:D.386, A:D.386 GLC-GLC.12: 15 residues within 4Å: Chain B: W.100, Y.146, H.169, I.170, H.200, I.248, R.287, R.325, D.386, G.387, M.388, N.389, L.390 Ligands: NHE.14, EDO.18 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:H.169, B:D.386, B:G.387, B:M.388, B:N.389, B:L.390 Water bridges: B:K.292 GLC-GLC.23: 15 residues within 4Å: Chain C: W.100, Y.146, H.169, I.170, H.200, I.248, R.287, R.325, D.386, G.387, M.388, N.389, L.390 Ligands: NHE.25, EDO.29 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.386, C:G.387, C:M.388, C:N.389, C:L.390 Water bridges: C:K.292, C:D.386, C:D.386 GLC-GLC.34: 15 residues within 4Å: Chain D: W.100, Y.146, H.169, I.170, H.200, I.248, R.287, R.325, D.386, G.387, M.388, N.389, L.390 Ligands: NHE.36, EDO.40 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:H.169, D:D.386, D:G.387, D:M.388, D:N.389, D:L.390 Water bridges: D:K.292

8 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.2: 8 residues within 4Å: Chain A: R.385, E.410, F.411 Chain B: E.176, M.179, R.184, R.214, L.215 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.215 Hydrogen bonds: B:E.176 Water bridges: B:R.214 Salt bridges: B:R.214, A:R.385 NHE.3: 10 residues within 4Å: Chain A: V.285, D.286, R.287, K.292, T.322, N.389, L.390, V.391 Ligands: GLC-GLC.1, GLC-GLC.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.285, A:V.391 Hydrogen bonds: A:L.390, A:V.391 Water bridges: A:K.292, A:N.389 Salt bridges: A:K.292 NHE.13: 8 residues within 4Å: Chain A: E.176, M.179, R.184, R.214, L.215 Chain B: R.385, E.410, F.411 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Salt bridges: B:R.385, A:R.214 Hydrophobic interactions: A:L.215 Hydrogen bonds: A:E.176 Water bridges: A:R.214 NHE.14: 10 residues within 4Å: Chain B: V.285, D.286, R.287, K.292, T.322, N.389, L.390, V.391 Ligands: GLC-GLC.12, GLC-GLC.12 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.285, B:V.391 Hydrogen bonds: B:L.390, B:V.391 Water bridges: B:K.292, B:N.389 Salt bridges: B:K.292 NHE.24: 8 residues within 4Å: Chain C: R.385, E.410, F.411 Chain D: E.176, M.179, R.184, R.214, L.215 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.215 Hydrogen bonds: D:E.176 Water bridges: D:R.214 Salt bridges: D:R.214, C:R.385 NHE.25: 10 residues within 4Å: Chain C: V.285, D.286, R.287, K.292, T.322, N.389, L.390, V.391 Ligands: GLC-GLC.23, GLC-GLC.23 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.285, C:V.391 Hydrogen bonds: C:L.390, C:V.391 Water bridges: C:K.292, C:N.389 Salt bridges: C:K.292 NHE.35: 8 residues within 4Å: Chain C: E.176, M.179, R.184, R.214, L.215 Chain D: R.385, E.410, F.411 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.215 Hydrogen bonds: C:E.176 Water bridges: C:R.214 Salt bridges: C:R.214, D:R.385 NHE.36: 10 residues within 4Å: Chain D: V.285, D.286, R.287, K.292, T.322, N.389, L.390, V.391 Ligands: GLC-GLC.34, GLC-GLC.34 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:V.285, D:V.391 Hydrogen bonds: D:L.390, D:V.391 Water bridges: D:K.292, D:N.389 Salt bridges: D:K.292

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

EDO.4: 4 residues within 4Å: Chain A: V.121, R.125, M.154, E.186 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: E.445, R.448, R.449, R.452 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain A: D.462, D.464 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: W.100, R.287, D.289, K.292, S.324, R.325 Ligands: GLC-GLC.1 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: A.259, R.260, R.265, V.374, C.398, S.400, D.401 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: Q.299, A.302, R.340, Q.341, H.344 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: L.288, P.323, S.324, E.326, Y.331, R.335, H.361 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: H.427, N.428, L.429, D.430 Chain B: Y.112, W.183 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain B: V.121, R.125, M.154, E.186 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: E.445, R.448, R.449, R.452 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain B: D.462, D.464 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain B: W.100, R.287, D.289, K.292, S.324, R.325 Ligands: GLC-GLC.12 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain B: A.259, R.260, R.265, V.374, C.398, S.400, D.401 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: Q.299, A.302, R.340, Q.341, H.344 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain B: L.288, P.323, S.324, E.326, Y.331, R.335, H.361 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain A: Y.112, W.183 Chain B: H.427, N.428, L.429, D.430 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain C: V.121, R.125, M.154, E.186 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain C: E.445, R.448, R.449, R.452 Ligand excluded by PLIP EDO.28: 2 residues within 4Å: Chain C: D.462, D.464 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain C: W.100, R.287, D.289, K.292, S.324, R.325 Ligands: GLC-GLC.23 Ligand excluded by PLIP EDO.30: 7 residues within 4Å: Chain C: A.259, R.260, R.265, V.374, C.398, S.400, D.401 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain C: Q.299, A.302, R.340, Q.341, H.344 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain C: L.288, P.323, S.324, E.326, Y.331, R.335, H.361 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain C: H.427, N.428, L.429, D.430 Chain D: Y.112, W.183 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain D: V.121, R.125, M.154, E.186 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain D: E.445, R.448, R.449, R.452 Ligand excluded by PLIP EDO.39: 2 residues within 4Å: Chain D: D.462, D.464 Ligand excluded by PLIP EDO.40: 7 residues within 4Å: Chain D: W.100, R.287, D.289, K.292, S.324, R.325 Ligands: GLC-GLC.34 Ligand excluded by PLIP EDO.41: 7 residues within 4Å: Chain D: A.259, R.260, R.265, V.374, C.398, S.400, D.401 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain D: Q.299, A.302, R.340, Q.341, H.344 Ligand excluded by PLIP EDO.43: 7 residues within 4Å: Chain D: L.288, P.323, S.324, E.326, Y.331, R.335, H.361 Ligand excluded by PLIP EDO.44: 6 residues within 4Å: Chain C: Y.112, W.183 Chain D: H.427, N.428, L.429, D.430 Ligand excluded by PLIP

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
A

C
A

D
A

Alpha,alpha-trehalose-phosphate synthase

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