Research workbench
Crystal structure of ustilago sphaerogena ribonuclease U2B
Analyse Crystal structure of ustilago sphaerogena ribonuclease U2B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AHS
- Type
- protein
- Length
- 336 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease U2
- EC
- 3.1.27.4
- UniProt
- P00654
- Ligands
- K, PO4
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonuclease U2 (EC 3.1.27.4) | protein | 114 | 11% helix, 25% strand | P00654 |
| C | Ribonuclease U2 (EC 3.1.27.4) | protein | 108 | 11% helix, 27% strand | P00654 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, C, B
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.72 | 0.80 | 63 | PO4 |
| 2 | 163 | 0.42 | 0.74 | 22 | PO4 |
| 3 | 62 | 0.38 | 0.79 | 19 | empty |
| 4 | 91 | 0.31 | 0.73 | 18 | empty |
| 5 | 57 | 0.28 | 0.74 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–C · 912 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 378 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 138 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
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 P00654
- Elsewhere: RCSB PDB 3AHS · PDBe 3AHS · UniProt P00654
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