SMTL ID : 5hvl.3 (2 other biounits)

Structure of Candida albicans trehalose-6-phosphate synthase in complex with UDP and validoxylamine A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.1: 12 residues within 4Å: Chain A: V.278, R.280, K.285, V.315, S.356, I.357, L.362, N.382, L.383, V.384, E.387 Ligands: VDM.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.278, A:V.315 Hydrogen bonds: A:I.357, A:Y.366, A:L.383, A:V.384, A:E.387 Water bridges: A:G.33, A:R.280, A:N.382 Salt bridges: A:R.280, A:K.285, A:K.285 UDP.4: 12 residues within 4Å: Chain B: V.278, R.280, K.285, V.315, S.356, I.357, L.362, N.382, L.383, V.384, E.387 Ligands: VDM.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.278, B:V.315 Hydrogen bonds: B:I.357, B:L.383, B:V.384, B:E.387 Water bridges: B:G.33, B:R.280 Salt bridges: B:R.280, B:K.285, B:K.285 UDP.7: 13 residues within 4Å: Chain C: V.278, R.280, K.285, V.315, S.356, I.357, L.362, Y.366, N.382, L.383, V.384, E.387 Ligands: VDM.8 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:V.278, C:V.315 Hydrogen bonds: C:I.357, C:Y.366, C:L.383, C:V.384 Water bridges: C:G.33, C:K.285, C:S.356 Salt bridges: C:R.280, C:K.285, C:K.285 UDP.10: 13 residues within 4Å: Chain D: V.278, R.280, K.285, V.315, S.356, I.357, L.362, Y.366, N.382, L.383, V.384, E.387 Ligands: VDM.11 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:V.278, D:V.315 Hydrogen bonds: D:I.357, D:Y.366, D:Y.366, D:L.383, D:V.384 Water bridges: D:G.33, D:K.285, D:S.356, D:N.382 Salt bridges: D:R.280, D:K.285, D:K.285

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.2: 17 residues within 4Å: Chain A: W.98, D.143, Y.144, H.145, H.171, T.172, H.202, I.242, R.280, I.284, R.318, D.379, G.380, M.381, N.382, L.383 Ligands: UDP.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.98, A:H.171 Hydrogen bonds: A:D.143, A:Y.144, A:H.171, A:R.280, A:R.318, A:G.380, A:M.381, A:N.382, A:L.383 Water bridges: A:H.145, A:D.379 VDM.5: 17 residues within 4Å: Chain B: W.98, D.143, Y.144, H.145, H.171, T.172, H.202, I.242, R.280, I.284, R.318, D.379, G.380, M.381, N.382, L.383 Ligands: UDP.4 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.98, B:H.171 Hydrogen bonds: B:D.143, B:D.143, B:Y.144, B:Y.144, B:H.171, B:R.280, B:R.318, B:D.379, B:G.380, B:M.381, B:N.382, B:L.383 Water bridges: B:H.145, B:D.379 VDM.8: 17 residues within 4Å: Chain C: W.98, D.143, Y.144, H.145, H.171, T.172, H.202, I.242, R.280, I.284, R.318, D.379, G.380, M.381, N.382, L.383 Ligands: UDP.7 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:W.98, C:H.171 Hydrogen bonds: C:D.143, C:D.143, C:Y.144, C:Y.144, C:R.280, C:R.318, C:D.379, C:D.379, C:G.380, C:M.381, C:N.382, C:L.383 Water bridges: C:Y.89 VDM.11: 17 residues within 4Å: Chain D: W.98, D.143, Y.144, H.145, H.171, T.172, H.202, I.242, R.280, I.284, R.318, D.379, G.380, M.381, N.382, L.383 Ligands: UDP.10 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:W.98, D:H.171 Hydrogen bonds: D:D.143, D:Y.144, D:H.171, D:R.280, D:R.318, D:D.379, D:G.380, D:M.381, D:N.382, D:L.383

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 9 residues within 4Å: Chain A: R.208, H.209 Chain B: S.176, S.177, R.208, H.209, S.212, R.216 Ligands: SO4.6 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.177, B:R.208, B:S.212 Salt bridges: B:H.209, A:R.208, A:H.209 SO4.6: 9 residues within 4Å: Chain A: S.176, S.177, R.208, H.209, S.212, R.216 Chain B: R.208, H.209 Ligands: SO4.3 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Salt bridges: B:R.208, B:H.209, A:H.209 Hydrogen bonds: A:S.177, A:R.208, A:S.212 SO4.9: 9 residues within 4Å: Chain C: S.176, S.177, H.209, S.212, R.216 Chain D: S.176, R.208, H.209 Ligands: SO4.12 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.177, C:S.212 Salt bridges: C:H.209, D:R.208, D:H.209 SO4.12: 9 residues within 4Å: Chain C: S.176, R.208, H.209 Chain D: S.176, S.177, H.209, S.212, R.216 Ligands: SO4.9 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Salt bridges: C:R.208, C:H.209, D:H.209 Hydrogen bonds: D:S.177, D:S.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miao, Y. et al., Structural and In Vivo Studies on Trehalose-6-Phosphate Synthase from Pathogenic Fungi Provide Insights into Its Catalytic Mechanism, Biological Necessity, and Potential for Novel Antifungal Drug Design. MBio (2017)

Release Date

2017-05-03

Peptides

Alpha,alpha-trehalose-phosphate synthase [UDP-forming]: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

Alpha,alpha-trehalose-phosphate synthase [UDP-forming]

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