Research workbench
Chromosomal trehalose-6-phosphate phosphatase from P. aeruginosa
Analyse Chromosomal trehalose-6-phosphate phosphatase from P. aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D3V
- Type
- protein
- Length
- 502 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trehalose phosphatase
- UniProt
- A0A1S1GKD7
- Ligands
- NI
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Trehalose phosphatase | protein | 251 | 38% helix, 26% strand | A0A1S1GKD7 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 3 copies · chains A, B
- ACY · Acetic acid · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.70 | 0.82 | 39 | NI, ACY |
| 2 | 430 | 0.68 | 0.80 | 39 | ACY, NI |
| 3 | 220 | 0.53 | 0.77 | 26 | empty |
| 4 | 181 | 0.49 | 0.76 | 25 | empty |
| 5 | 89 | 0.38 | 0.76 | 16 | EDO |
Interfaces
1 interface between chains.
- A–B · 1350 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6D3V · Chromosomal trehalose-6-phosphate phosphatase from P. aeruginosa · 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 A0A1S1GKD7
- Elsewhere: RCSB PDB 6D3V · PDBe 6D3V · UniProt A0A1S1GKD7
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