MolNFT v1 · #45422 · protein
Ensemble structure of the closed state of LYS63-linked diubiquitin in the absence of a ligand
2N2K: “Ensemble structure of the closed state of LYS63-linked diubiquitin in the absence of a ligand”. Solution nmr, 1 ligand (MTN), 2 pockets (best druggability 0.59). MolNFT v1 #45422 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 2N2K
- Type
- protein
- Length
- 147 residues
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin
- UniProt
- P0CG48
- Ligands
- MTN
- Pockets
- 2 · best druggability 0.59
Structure
solution nmr · 2 distinct chains · 24% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin | protein | 76 | 24% helix, 34% strand | P0CG48 |
| B | Ubiquitin | protein | 71 | 25% helix, 34% strand | P0CG48 |
Ligands and binding sites
- MTN · S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate · ligand · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.59 | 0.75 | 53 | empty |
| 2 | 509 | 0.58 | 0.74 | 47 | empty |
Interfaces
1 interface between chains.
- A–B · 76 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 isopeptide (covalent ligand, isopeptide).
Compared structures
- 2N2K · Ensemble structure of the closed state of Lys63-linked diubiquitin in the absence of a… · the same entry in another collection · chain A against A, TM-score 1.00
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 P0CG48
- Elsewhere: RCSB PDB 2N2K · PDBe 2N2K · UniProt P0CG48
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