Research workbench
Structure of ribonuclease yabj
Analyse Structure of ribonuclease yabj in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YU2
- Type
- protein
- Length
- 750 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Translation initiation inhibitor homologue
- UniProt
- A0A0H3JTJ5
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Translation initiation inhibitor homologue | protein | 128 | 30% helix, 29% strand | A0A0H3JTJ5 |
| B, D, E, F | Translation initiation inhibitor homologue | protein | 124 | 31% helix, 30% strand | A0A0H3JTJ5 |
| C | Translation initiation inhibitor homologue | protein | 126 | 31% helix, 29% strand | A0A0H3JTJ5 |
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.83 | 0.98 | 27 | empty |
| 2 | 166 | 0.82 | 0.97 | 27 | empty |
| 3 | 613 | 0.69 | 0.78 | 48 | empty |
| 4 | 210 | 0.65 | 0.83 | 23 | empty |
| 5 | 231 | 0.63 | 0.82 | 26 | empty |
Interfaces
8 interfaces between chains.
- A–C · 1094 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1011 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1006 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 999 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 999 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5YU2 · Structure of Ribonuclease YabJ · 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 A0A0H3JTJ5
- Elsewhere: RCSB PDB 5YU2 · PDBe 5YU2 · UniProt A0A0H3JTJ5
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