SMTL ID : 8z2t.1

Crystal structure of trehalose synthase from Deinococcus radiodurans complexed with validoxylamine A (VAA)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.83 Å

Oligo State

homo-tetramer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: N.107, D.181, L.182, Y.215, L.216, E.218 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.181, A:Y.215, A:L.216, A:E.218 CA.4: 6 residues within 4Å: Chain B: N.107, D.181, L.182, Y.215, L.216, E.218 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.181, B:Y.215, B:L.216, B:E.218 CA.7: 5 residues within 4Å: Chain C: N.107, D.181, Y.215, L.216, E.218 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.181, C:Y.215, C:L.216, C:E.218 CA.10: 6 residues within 4Å: Chain D: N.107, D.181, L.182, Y.215, L.216, E.218 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.181, D:Y.215, D:L.216, D:E.218

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.26, N.28, D.30, K.32, D.34, D.79 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.26, A:D.30, A:K.32, A:D.34 MG.5: 5 residues within 4Å: Chain B: D.26, N.28, D.30, K.32, D.34 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.26, B:D.30, B:K.32, B:D.34 MG.8: 6 residues within 4Å: Chain C: D.26, N.28, D.30, K.32, D.34, D.79 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.26, C:D.30, C:K.32, C:D.34 MG.11: 6 residues within 4Å: Chain D: D.26, N.28, D.30, K.32, D.34, D.79 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.26, D:D.30, D:D.30, D:K.32, D:D.34

4 x VDM: (1S,2S,3R,6S)-4-(HYDROXYMETHYL)-6-{[(1S,2S,3S,4R,5R)-2,3,4-TRIHYDROXY-5-(HYDROXYMETHYL)CYCLOHEXYL]AMINO}CYCLOHEX-4-ENE-1,2,3-TRIOL(Non-covalent)

VDM.3: 18 residues within 4Å: Chain A: D.65, Y.68, H.108, F.153, F.175, Q.179, R.209, D.211, Y.215, E.253, N.255, H.320, D.321, E.322, T.324, E.326, R.400, R.404 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.175 Hydrogen bonds: A:D.65, A:H.108, A:Q.179, A:R.209, A:R.209, A:D.211, A:Y.215, A:E.253, A:E.253, A:N.255, A:H.320, A:E.322, A:T.324, A:R.400, A:R.400, A:R.404 VDM.6: 17 residues within 4Å: Chain B: D.65, Y.68, H.108, F.153, F.175, Q.179, R.209, D.211, Y.215, E.253, N.255, H.320, D.321, E.322, T.324, E.326, R.400 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.175 Hydrogen bonds: B:D.65, B:H.108, B:Q.179, B:R.209, B:R.209, B:E.253, B:E.253, B:N.255, B:H.320, B:E.322, B:T.324, B:T.324, B:R.400, B:R.400, B:R.404 VDM.9: 17 residues within 4Å: Chain C: D.65, Y.68, H.108, F.153, F.175, Q.179, R.209, D.211, E.253, N.255, H.320, D.321, E.322, T.324, E.326, R.400, R.404 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:F.175 Hydrogen bonds: C:D.65, C:D.65, C:H.108, C:Q.179, C:R.209, C:R.209, C:Y.215, C:E.253, C:E.253, C:N.255, C:H.320, C:E.322, C:T.324, C:R.400, C:R.400, C:R.404 VDM.12: 16 residues within 4Å: Chain D: D.65, Y.68, H.108, F.153, Q.179, R.209, D.211, E.253, N.255, H.320, D.321, E.322, T.324, E.326, R.400, R.404 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:D.65, D:D.65, D:H.108, D:Q.179, D:R.209, D:R.209, D:E.253, D:E.253, D:N.255, D:H.320, D:E.322, D:E.326, D:R.400, D:R.400, D:R.404

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, L.C. et al., Structural and Mutational Analyses of Trehalose Synthase from Deinococcus radiodurans Reveal the Interconversion of Maltose-Trehalose Mechanism. J.Agric.Food Chem. (2024)

Release Date

2025-01-01

Peptides

maltose alpha-D-glucosyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

maltose alpha-D-glucosyltransferase

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