MolNFT v1 · #121436 · protein
Structure of candida albicans trehalose-6-phosphate synthase in complex with udp and validoxylamine a
5HVL · ALPHA,ALPHA-trehalose-phosphate synthase [udp-forming]: “Structure of candida albicans trehalose-6-phosphate synthase in complex with udp and validoxylamine a”. X-ray diffraction, 3 ligands (UDP, VDM, SO4), 8 pockets (best…
- PDB
- 5HVL
- Type
- protein
- Length
- 933 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ALPHA,ALPHA-trehalose-phosphate synthase [udp-forming]
- EC
- 2.4.1.15
- UniProt
- Q92410
- Ligands
- UDP, VDM, SO4
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ALPHA,ALPHA-trehalose-phosphate synthase [udp-forming] (EC 2.4.1.15) | protein | 467 | 49% helix, 19% strand | Q92410 |
| B | ALPHA,ALPHA-trehalose-phosphate synthase [udp-forming] (EC 2.4.1.15) | protein | 466 | 50% helix, 19% strand | Q92410 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- 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 · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.76 | 0.79 | 61 | UDP, VDM |
| 2 | 917 | 0.76 | 0.79 | 62 | UDP, VDM |
| 3 | 484 | 0.63 | 0.76 | 53 | empty |
| 4 | 78 | 0.44 | 0.80 | 20 | empty |
| 5 | 69 | 0.37 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 286 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5HVL · Structure of Candida albicans trehalose-6-phosphate synthase in complex with UDP and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q92410 · AlphaFold monomer V2.0 prediction for ALPHA,ALPHA-trehalose-phosphate synthase… · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q92410
- Elsewhere: RCSB PDB 5HVL · PDBe 5HVL · UniProt Q92410
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