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Crystal structure of an ALPHA,ALPHA-trehalose-phosphate synthase (udp- forming) from burkholderia vietnamiensis
Analyse Crystal structure of an ALPHA,ALPHA-trehalose-phosphate synthase (udp- forming)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TVG
- Type
- protein
- Length
- 3,621 residues
- Chains
- 8
- 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
- A4JGS8
- Ligands
- UDP, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 8 distinct chains · 49% 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 | 468 | 47% helix, 19% strand | A4JGS8 |
| B | ALPHA,ALPHA-trehalose-phosphate synthase (udp-forming) (EC 2.4.1.15) | protein | 454 | 49% helix, 20% strand | A4JGS8 |
| C | ALPHA,ALPHA-trehalose-phosphate synthase (udp-forming) (EC 2.4.1.15) | protein | 458 | 48% helix, 19% strand | A4JGS8 |
| D | ALPHA,ALPHA-trehalose-phosphate synthase (udp-forming) (EC 2.4.1.15) | protein | 456 | 48% helix, 19% strand | A4JGS8 |
| E | ALPHA,ALPHA-trehalose-phosphate synthase (udp-forming) (EC 2.4.1.15) | protein | 447 | 49% helix, 19% strand | A4JGS8 |
| F | ALPHA,ALPHA-trehalose-phosphate synthase (udp-forming) (EC 2.4.1.15) | protein | 456 | 49% helix, 19% strand | A4JGS8 |
| G | ALPHA,ALPHA-trehalose-phosphate synthase (udp-forming) (EC 2.4.1.15) | protein | 439 | 50% helix, 18% strand | A4JGS8 |
| H | ALPHA,ALPHA-trehalose-phosphate synthase (udp-forming) (EC 2.4.1.15) | protein | 443 | 49% helix, 19% strand | A4JGS8 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 3 copies · chains A, B, D
- GOL · Glycerol · additive · 13 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.78 | 0.80 | 62 | UDP, GOL |
| 2 | 930 | 0.77 | 0.79 | 60 | UDP, GOL |
| 3 | 916 | 0.76 | 0.79 | 63 | UDP, GOL |
| 4 | 838 | 0.75 | 0.79 | 59 | UDP, GOL |
| 5 | 800 | 0.73 | 0.78 | 58 | UDP, GOL |
Interfaces
10 interfaces between chains.
- D–H · 1336 Ų buried · 29 hydrogen bonds · protein-protein
- C–E · 1291 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1290 Ų buried · 32 hydrogen bonds · protein-protein
- F–G · 1267 Ų buried · 32 hydrogen bonds · protein-protein
- D–G · 1225 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5TVG · Crystal structure of an alpha,alpha-trehalose-phosphate synthase (UDP-forming) from… · 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 A4JGS8
- Elsewhere: RCSB PDB 5TVG · PDBe 5TVG · UniProt A4JGS8
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