Research workbench
Ubiquitin specific protease 11 USP11 - peptide F complex
Analyse Ubiquitin specific protease 11 USP11 - peptide F complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OK6
- Type
- protein
- Length
- 462 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 11; Ala-glu-gly-glu-phe-tyr-lys-leu-lys-ile-arg-thr…
- UniProt
- G5E9A6
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-terminal hydrolase 11 | protein | 219 | 22% helix, 28% strand | G5E9A6 |
| B | Ubiquitin carboxyl-terminal hydrolase 11 | protein | 217 | 23% helix, 29% strand | G5E9A6 |
| C | Ala-glu-gly-glu-phe-tyr-lys-leu-lys-ile-arg-thr-pro-aar | protein | 14 | 43% helix, 14% strand | — |
| D | Ala-glu-gly-glu-phe-tyr-lys-leu-lys-ile-arg-thr-pro-aar | protein | 12 | 33% helix, 8% strand | — |
Ligands and binding sites
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 | 1186 | 0.70 | 0.74 | 80 | GOL |
| 2 | 76 | 0.33 | 0.75 | 15 | EDO |
| 3 | 65 | 0.31 | 0.75 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 874 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 802 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 744 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5OK6 · Ubiquitin specific protease 11 USP11 - peptide F complex · 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 G5E9A6
- Elsewhere: RCSB PDB 5OK6 · PDBe 5OK6 · UniProt G5E9A6
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