MolNFT v1 · #135922 · protein
HHARI/ARIH1-UBCH7~UBIQUITIN
5UDH · E3 ubiquitin-protein ligase ARIH1: “HHARI/ARIH1-UBCH7~UBIQUITIN”. X-ray diffraction, 1 ligand (ZN), 12 pockets (best druggability 0.61). MolNFT v1 #135922 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5UDH
- Type
- protein
- Length
- 1,172 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase ARIH1; Ubiquitin-conjugating enzyme E2 L3; Ubiquitin C variant
- EC
- 2.3.2.-, 2.3.2.23
- UniProt
- Q9Y4X5, P68036, Q59EM9
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase ARIH1 (EC 2.3.2.-) | protein | 411 | 51% helix, 11% strand | Q9Y4X5 |
| C | Ubiquitin-conjugating enzyme E2 L3 (EC 2.3.2.23) | protein | 152 | 38% helix, 14% strand | P68036 |
| B | E3 ubiquitin-protein ligase ARIH1 (EC 2.3.2.-) | protein | 381 | 49% helix, 10% strand | Q9Y4X5 |
| D | Ubiquitin-conjugating enzyme E2 L3 (EC 2.3.2.23) | protein | 155 | 37% helix, 15% strand | P68036 |
| E | Ubiquitin C variant | protein | 73 | 16% helix, 27% strand | Q59EM9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.61 | 0.91 | 21 | empty |
| 2 | 427 | 0.60 | 0.75 | 41 | empty |
| 3 | 181 | 0.59 | 0.82 | 39 | empty |
| 4 | 89 | 0.58 | 0.87 | 25 | empty |
| 5 | 183 | 0.47 | 0.76 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–C · 749 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 722 Ų buried · 5 hydrogen bonds · protein-protein
- C–B · 418 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 401 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 233 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5UDH · HHARI/ARIH1-UBCH7~Ubiquitin · the same entry in another collection · chain E against E, TM-score 1.00
- P68036 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 L3 (P68036) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q9Y4X5 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase ARIH1 (Q9Y4X5) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q9Y4X5
- Every structure of UniProt P68036
- Every structure of UniProt Q59EM9
- Elsewhere: RCSB PDB 5UDH · PDBe 5UDH · UniProt Q9Y4X5 · UniProt P68036 · UniProt Q59EM9
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