Research workbench
RPN13 (19-132)-RPN2 (940-952) PY950-ub complex
Analyse RPN13 (19-132)-RPN2 (940-952) PY950-ub complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OI4
- Type
- protein
- Length
- 392 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proteasomal ubiquitin receptor ADRM1; Ubiquitin; 26S proteasome non-ATPase regulatory…
- UniProt
- Q16186, P0CG48, Q99460
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 15% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proteasomal ubiquitin receptor ADRM1 | protein | 111 | 14% helix, 48% strand | Q16186 |
| C, D | Ubiquitin | protein | 75 | 24% helix, 35% strand | P0CG48 |
| E | 26S proteasome non-ATPase regulatory subunit 1 | protein | 12 | 0% helix, 17% strand | Q99460 |
| B | Proteasomal ubiquitin receptor ADRM1 | protein | 108 | 12% helix, 48% strand | Q16186 |
| F | 26S proteasome non-ATPase regulatory subunit 1 | protein | 11 | 0% helix, 18% strand | Q99460 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, C, D, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.61 | 0.81 | 29 | empty |
| 2 | 85 | 0.39 | 0.77 | 16 | empty |
| 3 | 56 | 0.29 | 0.75 | 18 | empty |
| 4 | 60 | 0.29 | 0.74 | 13 | empty |
| 5 | 55 | 0.28 | 0.74 | 18 | EDO |
Interfaces
6 interfaces between chains.
- A–E · 788 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 776 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 447 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 443 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 432 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6OI4 · RPN13 (19-132)-RPN2 (940-952) pY950-Ub complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q16186 · AlphaFold monomer V2.0 prediction for proteasomal ubiquitin receptor ADRM1 (Q16186) · a predicted model of the same protein · chain B against A, TM-score 0.97
- Q99460 · AlphaFold monomer V2.0 prediction for 26S proteasome non-ATPase regulatory subunit 1… · a predicted model of the same protein · chain F against A, TM-score 0.48
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 Q16186
- Every structure of UniProt P0CG48
- Every structure of UniProt Q99460
- Elsewhere: RCSB PDB 6OI4 · PDBe 6OI4 · UniProt Q16186 · UniProt P0CG48 · UniProt Q99460
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.