Research workbench
Structure of DUP1 mutant H67A:UBIQUITIN complex
Analyse Structure of DUP1 mutant H67A:UBIQUITIN complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RYA
- Type
- protein
- Length
- 1,152 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Septation initiation protein; Polyubiquitin-C
- UniProt
- A0A3A6VNK6, P0CG48
- Pockets
- 13 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Septation initiation protein | protein | 308 | 53% helix, 5% strand | A0A3A6VNK6 |
| B, D, F | Polyubiquitin-C | protein | 76 | 24% helix, 30% strand | P0CG48 |
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 554 | 0.67 | 0.77 | 48 | empty |
| 2 | 395 | 0.65 | 0.79 | 37 | empty |
| 3 | 416 | 0.65 | 0.78 | 40 | empty |
| 4 | 366 | 0.60 | 0.77 | 53 | empty |
| 5 | 50 | 0.59 | 0.92 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1440 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1432 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1415 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 446 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 175 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6RYA · Structure of Dup1 mutant H67A:Ubiquitin 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 A0A3A6VNK6
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 6RYA · PDBe 6RYA · UniProt A0A3A6VNK6 · UniProt P0CG48
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