MolNFT v1 · #116598 · protein
Structural basis for the indispensable role of a unique zinc finger motif in LNX2 ubiquitination
5DIN · Ligand of numb protein X 2: “Structural basis for the indispensable role of a unique zinc finger motif in LNX2 ubiquitination”. X-ray diffraction, 1 ligand (ZN), 6 pockets (best druggability 0.45). MolNFT v1 #116598 on GenesisL1: 3D…
- PDB
- 5DIN
- Type
- protein
- Length
- 244 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ligand of numb protein X 2
- EC
- 6.3.2.19
- UniProt
- Q8N448
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ligand of numb protein X 2 (EC 6.3.2.19) | protein | 120 | 26% helix, 17% strand | Q8N448 |
| B | Ligand of numb protein X 2 (EC 6.3.2.19) | protein | 124 | 25% helix, 16% strand | Q8N448 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.45 | 0.82 | 15 | empty |
| 2 | 130 | 0.41 | 0.75 | 19 | empty |
| 3 | 122 | 0.41 | 0.75 | 22 | empty |
| 4 | 65 | 0.39 | 0.79 | 15 | empty |
| 5 | 80 | 0.36 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 694 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5DIN · Structural Basis for the Indispensable Role of a Unique Zinc Finger Motif in LNX2… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8N448 · AlphaFold monomer V2.0 prediction for ligand of numb protein X 2 (Q8N448) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8N448
- Elsewhere: RCSB PDB 5DIN · PDBe 5DIN · UniProt Q8N448
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