Research workbench
Structure of aspergillus fumigatus trehalose-6-phosphate synthase B in complex with udp and validoxylamine a
Analyse Structure of aspergillus fumigatus trehalose-6-phosphate synthase B in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HVO
- Type
- protein
- Length
- 1,823 residues
- Chains
- 4
- 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
- Q4WHW0
- Ligands
- UDP, VDM
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 48% 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 | 459 | 48% helix, 19% strand | Q4WHW0 |
| B | ALPHA,ALPHA-trehalose-phosphate synthase (udp-forming) (EC 2.4.1.15) | protein | 454 | 48% helix, 19% strand | Q4WHW0 |
| C | ALPHA,ALPHA-trehalose-phosphate synthase (udp-forming) (EC 2.4.1.15) | protein | 454 | 48% helix, 18% strand | Q4WHW0 |
| D | ALPHA,ALPHA-trehalose-phosphate synthase (udp-forming) (EC 2.4.1.15) | protein | 456 | 48% helix, 19% strand | Q4WHW0 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- 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 · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.80 | 0.82 | 82 | empty |
| 2 | 1010 | 0.80 | 0.81 | 80 | empty |
| 3 | 725 | 0.75 | 0.80 | 65 | empty |
| 4 | 936 | 0.75 | 0.78 | 65 | UDP, VDM |
| 5 | 662 | 0.74 | 0.80 | 78 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1435 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1423 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 478 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 442 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 136 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5HVO · Structure of Aspergillus fumigatus trehalose-6-phosphate synthase B in complex with UDP… · the same entry in another collection · chain D against D, TM-score 1.00
- Q4WHW0 · AlphaFold monomer V2.0 prediction for ALPHA,ALPHA-trehalose-phosphate synthase… · a predicted model of the same protein · chain D 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 Q4WHW0
- Elsewhere: RCSB PDB 5HVO · PDBe 5HVO · UniProt Q4WHW0
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