Research workbench
Crystal structure of pspto -psp protein in complex with D-beta-glucose from pseudomonas syringae pv. tomato str. DC3000
Analyse Crystal structure of pspto -psp protein in complex with D-beta-glucose from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K0T
- Type
- protein
- Length
- 370 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoribonuclease L-psp, putative
- UniProt
- Q88BE5
- Ligands
- BGC
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endoribonuclease L-psp, putative | protein | 123 | 28% helix, 32% strand | Q88BE5 |
| C | Endoribonuclease L-psp, putative | protein | 124 | 31% helix, 33% strand | Q88BE5 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.80 | 0.97 | 36 | empty |
| 2 | 115 | 0.65 | 0.89 | 22 | BGC |
| 3 | 112 | 0.64 | 0.89 | 20 | BGC |
| 4 | 110 | 0.63 | 0.87 | 20 | BGC |
| 5 | 64 | 0.31 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 882 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 879 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 862 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3K0T · Crystal structure of PSPTO -PSP protein in complex with D-beta-Glucose from Pseudomonas… · 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 Q88BE5
- Elsewhere: RCSB PDB 3K0T · PDBe 3K0T · UniProt Q88BE5
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