MolNFT v1 · #153350 · protein
TPS1/UDP/T6P complex
6JBR · Trehalose-6-phosphate synthase: “TPS1/UDP/T6P complex”. X-ray diffraction, 3 ligands (UDP, GLC, G6P), 20 pockets (best druggability 0.82). MolNFT v1 #153350 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JBR
- Type
- protein
- Length
- 3,720 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trehalose-6-phosphate synthase
- EC
- 2.4.1.15
- UniProt
- G4NHF4
- Ligands
- UDP, GLC, G6P
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, F, H, K, M, O | Trehalose-6-phosphate synthase (EC 2.4.1.15) | protein | 465 | 48% helix, 18% strand | G4NHF4 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 8 copies · chains A, B, D, F, H, K, M, O
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B, D, F, H, K, M, O
- G6P · 6-O-phosphono-alpha-D-glucopyranose · sugar · 8 copies · chains A, B, D, F, H, K, M, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.82 | 0.87 | 69 | GLC, G6P, UDP |
| 2 | 749 | 0.82 | 0.85 | 67 | GLC, G6P, UDP |
| 3 | 1188 | 0.81 | 0.83 | 107 | GLC, G6P, UDP |
| 4 | 846 | 0.81 | 0.83 | 71 | GLC, G6P, UDP |
| 5 | 800 | 0.81 | 0.84 | 72 | GLC, G6P, UDP |
Interfaces
9 interfaces between chains.
- B–D · 1226 Ų buried · 15 hydrogen bonds · protein-protein
- A–O · 1217 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1216 Ų buried · 19 hydrogen bonds · protein-protein
- H–K · 1202 Ų buried · 21 hydrogen bonds · protein-protein
- D–O · 1201 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan (glycosylation).
Compared structures
- 6JBR · Tps1/UDP/T6P complex · the same entry in another collection · chain A against A, TM-score 1.00
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 G4NHF4
- Elsewhere: RCSB PDB 6JBR · PDBe 6JBR · UniProt G4NHF4
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