Research workbench
Structural basis of the flanking zinc-finger motifs crucial for the E3 ligase activity of the LNX1 ring domain
Analyse Structural basis of the flanking zinc-finger motifs crucial for the E3 ligase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H7S
- Type
- protein
- Length
- 696 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-like 1; E3 ubiquitin-protein ligase lnx; Ubiquitin-conjugating enzyme E2 N
- EC
- 2.3.2.27, 2.3.2.23
- UniProt
- P0CG47, Q8TBB1, P61088
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, F | Ubiquitin-like 1 | protein | 76 | 24% helix, 30% strand | P0CG47 |
| D, B | E3 ubiquitin-protein ligase lnx (EC 2.3.2.27) | protein | 124 | 32% helix, 16% strand | Q8TBB1 |
| A, C | Ubiquitin-conjugating enzyme E2 N (EC 2.3.2.23) | protein | 148 | 34% helix, 18% strand | P61088 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains D, 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 | 73 | 0.74 | 0.98 | 20 | empty |
| 2 | 73 | 0.72 | 0.96 | 20 | empty |
| 3 | 366 | 0.62 | 0.78 | 42 | empty |
| 4 | 260 | 0.62 | 0.80 | 27 | empty |
| 5 | 188 | 0.47 | 0.75 | 28 | empty |
Interfaces
9 interfaces between chains.
- A–F · 968 Ų buried · 14 hydrogen bonds · protein-protein
- E–C · 930 Ų buried · 13 hydrogen bonds · protein-protein
- D–B · 728 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 696 Ų buried · 4 hydrogen bonds · protein-protein
- D–C · 680 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5H7S · Structural basis of the flanking zinc-finger motifs crucial for the E3 ligase activity of… · the same entry in another collection · chain C against C, TM-score 1.00
- Q8TBB1 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase lnx (Q8TBB1) · a predicted model of the same protein · chain D against A, TM-score 0.98
- P61088 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 N (P61088) · a predicted model of the same protein · chain A 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 P0CG47
- Every structure of UniProt Q8TBB1
- Every structure of UniProt P61088
- Elsewhere: RCSB PDB 5H7S · PDBe 5H7S · UniProt P0CG47 · UniProt Q8TBB1 · UniProt P61088
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