Research workbench
Crystal structure of baculovirus RNA 5'-phosphatase complexed with phosphate
Analyse Crystal structure of baculovirus RNA 5'-phosphatase complexed with phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YN9
- Type
- protein
- Length
- 496 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polynucleotide 5'-phosphatase
- EC
- 3.1.3.33
- UniProt
- P24656
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polynucleotide 5'-phosphatase (EC 3.1.3.33) | protein | 168 | 44% helix, 13% strand | P24656 |
| B | Polynucleotide 5'-phosphatase (EC 3.1.3.33) | protein | 169 | 44% helix, 12% strand | P24656 |
| C | Polynucleotide 5'-phosphatase (EC 3.1.3.33) | protein | 159 | 42% helix, 13% strand | P24656 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.49 | 0.77 | 38 | empty |
| 2 | 81 | 0.39 | 0.78 | 22 | empty |
| 3 | 86 | 0.36 | 0.76 | 22 | empty |
| 4 | 57 | 0.32 | 0.76 | 13 | empty |
| 5 | 51 | 0.26 | 0.74 | 12 | empty |
Interfaces
2 interfaces between chains.
- A–C · 619 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 198 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1YN9 · Crystal structure of baculovirus RNA 5'-phosphatase complexed with phosphate · 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 P24656
- Elsewhere: RCSB PDB 1YN9 · PDBe 1YN9 · UniProt P24656
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