MolNFT v1 · #121437 · protein
Structure of aspergillus fumigatus trehalose-6-phosphate synthase a in complex with udp and validoxylamine a
5HVM · ALPHA,ALPHA-trehalose-phosphate synthase (udp-forming): “Structure of aspergillus fumigatus trehalose-6-phosphate synthase a in complex with udp and validoxylamine a”. X-ray diffraction, 2 ligands (UDP, VDM), 8 pockets (best…
- PDB
- 5HVM
- Type
- protein
- Length
- 898 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
- Q4WLM9
- Ligands
- UDP, VDM
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ALPHA,ALPHA-trehalose-phosphate synthase (udp-forming) (EC 2.4.1.15) | protein | 446 | 49% helix, 17% strand | Q4WLM9 |
| B | ALPHA,ALPHA-trehalose-phosphate synthase (udp-forming) (EC 2.4.1.15) | protein | 452 | 48% helix, 18% strand | Q4WLM9 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 832 | 0.75 | 0.79 | 53 | UDP, VDM |
| 2 | 955 | 0.74 | 0.77 | 77 | UDP, VDM |
| 3 | 160 | 0.67 | 0.86 | 21 | empty |
| 4 | 302 | 0.62 | 0.79 | 26 | empty |
| 5 | 58 | 0.51 | 0.86 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1208 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5HVM · Structure of Aspergillus fumigatus trehalose-6-phosphate synthase A in complex with UDP… · the same entry in another collection · chain A against A, TM-score 1.00
- Q4WLM9 · 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 Q4WLM9
- Elsewhere: RCSB PDB 5HVM · PDBe 5HVM · UniProt Q4WLM9
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