Research workbench
Crystal structure of the escherichia COLI nucleosidase ppnn (apo form)
Analyse Crystal structure of the escherichia COLI nucleosidase ppnn (apo form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GFL
- Type
- protein
- Length
- 860 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PYRIMIDINE/PURINE nucleotide 5'-monophosphate nucleosidase
- EC
- 3.2.2.-, 3.2.2.10, 3.2.2.4
- UniProt
- P0ADR8
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PYRIMIDINE/PURINE nucleotide 5'-monophosphate nucleosidase (EC 3.2.2.-, 3.2.2.10, 3.2.2.4) | protein | 431 | 51% helix, 13% strand | P0ADR8 |
| B | PYRIMIDINE/PURINE nucleotide 5'-monophosphate nucleosidase (EC 3.2.2.-, 3.2.2.10, 3.2.2.4) | protein | 429 | 51% helix, 12% strand | P0ADR8 |
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.78 | 0.80 | 85 | empty |
| 2 | 102 | 0.75 | 0.96 | 31 | empty |
| 3 | 57 | 0.67 | 0.96 | 25 | empty |
| 4 | 118 | 0.65 | 0.88 | 24 | empty |
| 5 | 168 | 0.52 | 0.79 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1346 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6GFL · Crystal structure of the Escherichia coli nucleosidase PpnN (apo form) · the same entry in another collection · chain A against A, TM-score 1.00
- P0ADR8 · AlphaFold monomer V2.0 prediction for PYRIMIDINE/PURINE nucleotide 5'-monophosphate… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P0ADR8
- Elsewhere: RCSB PDB 6GFL · PDBe 6GFL · UniProt P0ADR8
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