Research workbench
Crystal structure of putative glycerophosphoryl diester phosphodiesterase (17743486) from agrobacterium tumefaciens str. C58 (dupont) at 1.80 a resolution
Analyse Crystal structure of putative glycerophosphoryl diester phosphodiesterase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KS6
- Type
- protein
- Length
- 993 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerophosphoryl diester phosphodiesterase
- UniProt
- A9CLR1
- Ligands
- UNL, MG, CL
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerophosphoryl diester phosphodiesterase | protein | 250 | 44% helix, 21% strand | A9CLR1 |
| B | Glycerophosphoryl diester phosphodiesterase | protein | 249 | 42% helix, 21% strand | A9CLR1 |
| C | Glycerophosphoryl diester phosphodiesterase | protein | 248 | 43% helix, 21% strand | A9CLR1 |
| D | Glycerophosphoryl diester phosphodiesterase | protein | 246 | 43% helix, 21% strand | A9CLR1 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A
- ACT · Acetate ion · additive · 6 copies · chains A, D, B, C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1065 | 0.72 | 0.76 | 118 | empty |
| 2 | 223 | 0.47 | 0.73 | 34 | empty |
| 3 | 127 | 0.44 | 0.77 | 25 | UNL, MG, ACT |
| 4 | 126 | 0.42 | 0.76 | 27 | UNL, ACT |
| 5 | 54 | 0.37 | 0.80 | 15 | UNL, MG, ACT |
Interfaces
4 interfaces between chains.
- A–D · 677 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 406 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 195 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 133 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 3KS6 · Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (17743486) 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 A9CLR1
- Elsewhere: RCSB PDB 3KS6 · PDBe 3KS6 · UniProt A9CLR1
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