MolNFT v1 · #129358 · protein
K33-specific affimer bound to K33 diub
5OHV · Ubiquitin: “K33-specific affimer bound to K33 diub”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.73). MolNFT v1 #129358 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5OHV
- Type
- protein
- Length
- 327 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; K33-specific affimer
- UniProt
- P0CG48
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ubiquitin | protein | 74 | 20% helix, 31% strand | P0CG48 |
| D | K33-specific affimer | protein | 90 | 21% helix, 62% strand | — |
| B | K33-specific affimer | protein | 89 | 21% helix, 63% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · 4 copies · chains A, D, C, B
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 | 57 | 0.73 | 0.98 | 12 | empty |
| 2 | 99 | 0.38 | 0.75 | 17 | empty |
| 3 | 54 | 0.33 | 0.78 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–C · 769 Ų buried · 6 hydrogen bonds · protein-protein
- D–B · 714 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 508 Ų buried · 4 hydrogen bonds · protein-protein
- C–B · 494 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 66 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5OHV · K33-specific affimer bound to K33 diUb · 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 P0CG48
- Elsewhere: RCSB PDB 5OHV · PDBe 5OHV · UniProt P0CG48
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