Research workbench
Crystal structure of the mouse RAP80 uims in complex with LYS63-linked di-ubiquitin
Analyse Crystal structure of the mouse RAP80 uims in complex with LYS63-linked… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A1Q
- Type
- protein
- Length
- 389 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin; Ubiquitin interaction motif-containing protein 1
- UniProt
- P62991, Q5U5Q9
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin | protein | 73 | 25% helix, 34% strand | P62991 |
| B, E | Ubiquitin | protein | 76 | 24% helix, 34% strand | P62991 |
| C, F | Ubiquitin interaction motif-containing protein 1 | protein | 45 | 87% helix, 0% strand | Q5U5Q9 |
| D | Ubiquitin | protein | 74 | 24% helix, 34% strand | P62991 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.59 | 0.75 | 34 | empty |
| 2 | 132 | 0.41 | 0.75 | 23 | empty |
| 3 | 78 | 0.40 | 0.79 | 18 | empty |
| 4 | 73 | 0.33 | 0.75 | 16 | empty |
Interfaces
9 interfaces between chains.
- E–F · 667 Ų buried · 3 hydrogen bonds · protein-protein
- D–F · 624 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 535 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 497 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 338 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- 3A1Q · Crystal structure of the mouse RAP80 UIMs in complex with Lys63-linked di-ubiquitin · the same entry in another collection · chain C against C, TM-score 1.00
- Q5U5Q9 · AlphaFold monomer V2.0 prediction for BRCA1-a complex subunit RAP80 (Q5U5Q9) · a predicted model of the same protein · chain C against A, TM-score 0.80
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 P62991
- Every structure of UniProt Q5U5Q9
- Elsewhere: RCSB PDB 3A1Q · PDBe 3A1Q · UniProt P62991 · UniProt Q5U5Q9
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