MolNFT v1 · #60894 · protein
Crystal structure of ribonuclease SA2 with exo-2',3'- cyclophosphorotioate
3D5I: “Crystal structure of ribonuclease SA2 with exo-2',3'- cyclophosphorotioate”. X-ray diffraction, 2 ligands (SGP, SO4), 3 pockets (best druggability 0.63). MolNFT v1 #60894 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3D5I
- Type
- protein
- Length
- 279 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease
- EC
- 3.1.4.8
- UniProt
- Q53752
- Ligands
- SGP, SO4
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease (EC 3.1.4.8) | protein | 92 | 15% helix, 25% strand | Q53752 |
| B | Ribonuclease (EC 3.1.4.8) | protein | 97 | 14% helix, 24% strand | Q53752 |
| C | Ribonuclease (EC 3.1.4.8) | protein | 90 | 16% helix, 27% strand | Q53752 |
Ligands and binding sites
- SGP · Guanosine-2',3'-cyclophosphorothioate · ligand · chains B
- SO4 · Sulfate ion · ion · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 181 | 0.63 | 0.85 | 38 | empty |
| 2 | 150 | 0.46 | 0.77 | 29 | SO4 |
| 3 | 55 | 0.28 | 0.74 | 18 | empty |
Interfaces
2 interfaces between chains.
- B–C · 851 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 505 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3D5I · Crystal structure of ribonuclease Sa2 with exo-2',3'-cyclophosphorotioate · 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 Q53752
- Elsewhere: RCSB PDB 3D5I · PDBe 3D5I · UniProt Q53752
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