MolNFT v1 · #125255 · protein
Structure of mycobacterium thermoresistibile trehalose-6-phosphate synthase in a ternary complex with ADP and fructose-6-phosphate
5L3K · ALPHA,ALPHA-trehalose-phosphate synthase: “Structure of mycobacterium thermoresistibile trehalose-6-phosphate synthase in a ternary complex with ADP and…”. X-ray diffraction, 3 ligands (ADP, F6P, PO4), 20 pockets (best druggability…
- PDB
- 5L3K
- Type
- protein
- Length
- 3,597 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ALPHA,ALPHA-trehalose-phosphate synthase
- UniProt
- A0A117IMA6
- Ligands
- ADP, F6P, PO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 8 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ALPHA,ALPHA-trehalose-phosphate synthase | protein | 448 | 46% helix, 18% strand | A0A117IMA6 |
| B | ALPHA,ALPHA-trehalose-phosphate synthase | protein | 458 | 45% helix, 19% strand | A0A117IMA6 |
| C | ALPHA,ALPHA-trehalose-phosphate synthase | protein | 444 | 47% helix, 17% strand | A0A117IMA6 |
| D | ALPHA,ALPHA-trehalose-phosphate synthase | protein | 462 | 45% helix, 21% strand | A0A117IMA6 |
| E | ALPHA,ALPHA-trehalose-phosphate synthase | protein | 461 | 45% helix, 20% strand | A0A117IMA6 |
| F | ALPHA,ALPHA-trehalose-phosphate synthase | protein | 455 | 46% helix, 20% strand | A0A117IMA6 |
| G | ALPHA,ALPHA-trehalose-phosphate synthase | protein | 419 | 48% helix, 16% strand | A0A117IMA6 |
| H | ALPHA,ALPHA-trehalose-phosphate synthase | protein | 450 | 45% helix, 20% strand | A0A117IMA6 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- F6P · 6-O-phosphono-beta-D-fructofuranose · ligand · 5 copies · chains B, C, D, E, F
- PO4 · Phosphate ion · ion · 6 copies · chains B, D, F, H
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C, 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 | 538 | 0.82 | 0.88 | 62 | ADP, F6P |
| 2 | 589 | 0.81 | 0.86 | 59 | ADP, F6P |
| 3 | 571 | 0.81 | 0.86 | 63 | ADP, F6P |
| 4 | 665 | 0.81 | 0.85 | 65 | ADP, F6P |
| 5 | 702 | 0.80 | 0.84 | 70 | ADP, F6P |
Interfaces
11 interfaces between chains.
- E–F · 1083 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1076 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1070 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1069 Ų buried · 15 hydrogen bonds · protein-protein
- E–H · 961 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5L3K · Structure of Mycobacterium thermoresistibile trehalose-6-phosphate synthase in a ternary… · 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 A0A117IMA6
- Elsewhere: RCSB PDB 5L3K · PDBe 5L3K · UniProt A0A117IMA6
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