Research workbench
Insight into the mechanism of enzymatic glycosyltransfer with retention through the synthesis and analysis of bisubstrate glycomimetics of trehalose-6-phosphate synthase
Analyse Insight into the mechanism of enzymatic glycosyltransfer with retention through… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WTX
- Type
- protein
- Length
- 1,807 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
- P31677
- Ligands
- UDP, VDO
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha, alpha-trehalose-phosphate synthase [udp- forming] (EC 2.4.1.15) | protein | 456 | 47% helix, 21% strand | P31677 |
| B | Alpha, alpha-trehalose-phosphate synthase [udp- forming] (EC 2.4.1.15) | protein | 454 | 48% helix, 20% strand | P31677 |
| C | Alpha, alpha-trehalose-phosphate synthase [udp- forming] (EC 2.4.1.15) | protein | 440 | 48% helix, 20% strand | P31677 |
| D | Alpha, alpha-trehalose-phosphate synthase [udp- forming] (EC 2.4.1.15) | protein | 457 | 48% helix, 20% strand | P31677 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- VDO · [(1R,2R,3S,4S,5S)-2,3,4-trihydroxy-5-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}cyclohexyl]methyl dihydrogen phosphate · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.83 | 0.88 | 76 | EDO, UDP, VDO |
| 2 | 566 | 0.80 | 0.86 | 67 | EDO, UDP, VDO |
| 3 | 757 | 0.75 | 0.80 | 51 | UDP, VDO |
| 4 | 717 | 0.73 | 0.79 | 47 | UDP, VDO |
| 5 | 651 | 0.72 | 0.79 | 79 | EDO |
Interfaces
4 interfaces between chains.
- A–B · 1139 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1132 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1122 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1106 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2WTX · Insight into the mechanism of enzymatic glycosyltransfer with retention through the… · the same entry in another collection · chain D against D, TM-score 1.00
- P31677 · AlphaFold monomer V2.0 prediction for trehalose-6-phosphate synthase (P31677) · a predicted model of the same protein · chain C 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 P31677
- Elsewhere: RCSB PDB 2WTX · PDBe 2WTX · UniProt P31677
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