Research workbench
Crystal structure of a linear-specific ubiquitin Fab bound to linear ubiquitin
Analyse Crystal structure of a linear-specific ubiquitin Fab bound to linear ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U30
- Type
- protein
- Length
- 1,152 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Linear di-ubiquitin; Light chain Fab; Heavy chain Fab
- UniProt
- P0CG48
- Pockets
- 13 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Linear di-ubiquitin | protein | 149 | 24% helix, 36% strand | P0CG48 |
| B, E | Light chain Fab | protein | 211 | 6% helix, 47% strand | — |
| C, F | Heavy chain Fab | protein | 218 | 4% helix, 51% strand | — |
| D | Linear di-ubiquitin | protein | 145 | 25% helix, 32% strand | P0CG48 |
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.60 | 0.76 | 44 | empty |
| 2 | 455 | 0.59 | 0.75 | 47 | empty |
| 3 | 473 | 0.57 | 0.73 | 54 | empty |
| 4 | 153 | 0.54 | 0.80 | 25 | empty |
| 5 | 75 | 0.40 | 0.79 | 21 | empty |
Interfaces
8 interfaces between chains.
- E–F · 1848 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1822 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 832 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 797 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 414 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3U30 · Crystal structure of a linear-specific Ubiquitin fab bound to linear ubiquitin · the same entry in another collection · chain E against E, 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 3U30 · PDBe 3U30 · UniProt P0CG48
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