Research workbench
Trehalose-6-phosphate synthase, GDP-glucose-dependent otsa
Analyse Trehalose-6-phosphate synthase, GDP-glucose-dependent otsa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LQD
- Type
- protein
- Length
- 1,771 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ALPHA,ALPHA-trehalose-phosphate synthase
- EC
- 2.4.1.36
- UniProt
- F2RH01
- Pockets
- 11 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | ALPHA,ALPHA-trehalose-phosphate synthase (EC 2.4.1.36) | protein | 446 | 49% helix, 17% strand | F2RH01 |
| B | ALPHA,ALPHA-trehalose-phosphate synthase (EC 2.4.1.36) | protein | 432 | 49% helix, 17% strand | F2RH01 |
| D | ALPHA,ALPHA-trehalose-phosphate synthase (EC 2.4.1.36) | protein | 447 | 49% helix, 16% strand | F2RH01 |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.74 | 0.77 | 66 | MES |
| 2 | 996 | 0.74 | 0.77 | 69 | MES |
| 3 | 666 | 0.73 | 0.80 | 76 | empty |
| 4 | 637 | 0.73 | 0.80 | 68 | empty |
| 5 | 995 | 0.73 | 0.76 | 66 | MES |
Interfaces
2 interfaces between chains.
- B–D · 1390 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 1387 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 5LQD · Trehalose-6-phosphate synthase, GDP-glucose-dependent OtsA · 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 F2RH01
- Elsewhere: RCSB PDB 5LQD · PDBe 5LQD · UniProt F2RH01
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