MolNFT v1 · #136726 · protein
Crystal structure of the RPN13 pru-RPN2 (932-953)-ubiquitin complex
5V1Z · Proteasomal ubiquitin receptor ADRM1: “Crystal structure of the RPN13 pru-RPN2 (932-953)-ubiquitin complex”. X-ray diffraction, 4 pockets (best druggability 0.62). MolNFT v1 #136726 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5V1Z
- Type
- protein
- Length
- 393 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
- 4 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proteasomal ubiquitin receptor ADRM1 | protein | 112 | 14% helix, 46% strand | Q16186 |
| B | Proteasomal ubiquitin receptor ADRM1 | protein | 112 | 12% helix, 47% strand | Q16186 |
| C | Ubiquitin | protein | 72 | 21% helix, 36% strand | P0CG47 |
| D | Ubiquitin | protein | 73 | 25% helix, 36% strand | P0CG47 |
| F, E | 26S proteasome non-ATPase regulatory subunit 1 | protein | 12 | 0% helix, 17% strand | Q99460 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.62 | 0.82 | 23 | empty |
| 2 | 473 | 0.61 | 0.75 | 57 | empty |
| 3 | 60 | 0.38 | 0.79 | 19 | empty |
| 4 | 60 | 0.30 | 0.75 | 16 | empty |
Interfaces
7 interfaces between chains.
- B–F · 824 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 758 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 527 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 465 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 412 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5V1Z · Crystal structure of the RPN13 PRU-RPN2 (932-953)-ubiquitin complex · the same entry in another collection · chain E against E, 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 0.43
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 5V1Z · PDBe 5V1Z · UniProt Q16186 · UniProt P0CG47 · UniProt Q99460
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