Research workbench
RICE_OTUB_LIKE_CATALYTIC domain
Analyse RICE_OTUB_LIKE_CATALYTIC domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K9N
- Type
- protein
- Length
- 966 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin thioesterase
- EC
- 3.4.19.12
- UniProt
- B9G207
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin thioesterase (EC 3.4.19.12) | protein | 242 | 55% helix, 14% strand | B9G207 |
| B | Ubiquitin thioesterase (EC 3.4.19.12) | protein | 241 | 57% helix, 15% strand | B9G207 |
| C | Ubiquitin thioesterase (EC 3.4.19.12) | protein | 240 | 55% helix, 13% strand | B9G207 |
| D | Ubiquitin thioesterase (EC 3.4.19.12) | protein | 243 | 56% helix, 14% strand | B9G207 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1040 | 0.80 | 0.81 | 83 | empty |
| 2 | 282 | 0.56 | 0.77 | 33 | empty |
| 3 | 126 | 0.46 | 0.78 | 20 | empty |
| 4 | 60 | 0.45 | 0.83 | 14 | empty |
| 5 | 86 | 0.37 | 0.76 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–B · 754 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 507 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 98 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 70 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6K9N · Rice_OTUB_like_catalytic domain · 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 B9G207
- Elsewhere: RCSB PDB 6K9N · PDBe 6K9N · UniProt B9G207
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