Research workbench
Crystal structure of the ternary RPN13 pru-RPN2 (940-953)-ubiquitin complex
Analyse Crystal structure of the ternary RPN13 pru-RPN2 (940-953)-ubiquitin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V1Y
- Type
- protein
- Length
- 398 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, P0CG47, Q99460
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 15% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proteasomal ubiquitin receptor ADRM1 | protein | 114 | 11% helix, 46% strand | Q16186 |
| B | Proteasomal ubiquitin receptor ADRM1 | protein | 113 | 12% helix, 47% strand | Q16186 |
| C | Ubiquitin | protein | 72 | 25% helix, 36% strand | P0CG47 |
| D | Ubiquitin | protein | 73 | 21% helix, 36% strand | P0CG47 |
| E | 26S proteasome non-ATPase regulatory subunit 1 | protein | 14 | 0% helix, 14% strand | Q99460 |
| F | 26S proteasome non-ATPase regulatory subunit 1 | protein | 12 | 0% helix, 17% strand | Q99460 |
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 | 687 | 0.74 | 0.80 | 65 | empty |
| 2 | 128 | 0.43 | 0.76 | 24 | empty |
| 3 | 81 | 0.38 | 0.77 | 18 | empty |
| 4 | 63 | 0.37 | 0.78 | 20 | empty |
| 5 | 52 | 0.28 | 0.75 | 14 | empty |
Interfaces
7 interfaces between chains.
- B–F · 821 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 806 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 437 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 412 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 364 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5V1Y · Crystal structure of the ternary RPN13 PRU-RPN2 (940-953)-ubiquitin 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 0.96
- 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 0.36
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 P0CG47
- Every structure of UniProt Q99460
- Elsewhere: RCSB PDB 5V1Y · PDBe 5V1Y · UniProt Q16186 · UniProt P0CG47 · UniProt Q99460
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