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The crystal structure of a 2,3-cyclic nucleotide 2- PHOSPHODIESTERASE/3-nucleotidase bifunctional periplasmic precursor protein from klebsiella pneumoniae subsp. pneumoniae mgh 78578
Analyse The crystal structure of a 2,3-cyclic nucleotide 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JYF
- Type
- protein
- Length
- 671 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2',3'-cyclic nucleotide 2'-PHOSPHODIESTERASE/3'- nucleotidase bifunctional periplasmic…
- UniProt
- A6THC4
- Ligands
- TAM, MN, SO4
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2',3'-cyclic nucleotide 2'-PHOSPHODIESTERASE/3'- nucleotidase bifunctional periplasmic protein | protein | 336 | 26% helix, 29% strand | A6THC4 |
| B | 2',3'-cyclic nucleotide 2'-PHOSPHODIESTERASE/3'- nucleotidase bifunctional periplasmic protein | protein | 335 | 27% helix, 29% strand | A6THC4 |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains B
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 9 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 540 | 0.62 | 0.75 | 62 | EPE, GOL |
| 2 | 78 | 0.34 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 303 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3JYF · The crystal structure of a 2,3-cyclic nucleotide 2-phosphodiesterase/3-nucleotidase… · 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 A6THC4
- Elsewhere: RCSB PDB 3JYF · PDBe 3JYF · UniProt A6THC4
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