MolNFT v1 · #94772 · protein
Crystal structure of trichinella spiralis UCH37 catalytic domain bound to ubiquitin vinyl methyl ester
4I6N · Ubiquitin carboxyl-hydrolase: “Crystal structure of trichinella spiralis UCH37 catalytic domain bound to ubiquitin vinyl methyl ester”. X-ray diffraction, 2 ligands (GVE, NA), 6 pockets (best druggability 0.76). MolNFT v1 #94772 on…
- PDB
- 4I6N
- Type
- protein
- Length
- 586 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-hydrolase; Ubiquitin
- UniProt
- P0CG48
- Ligands
- GVE, NA
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin carboxyl-hydrolase | protein | 219 | 37% helix, 21% strand | — |
| B, D | Ubiquitin | protein | 75 | 24% helix, 35% strand | P0CG48 |
| C | Ubiquitin carboxyl-hydrolase | protein | 217 | 36% helix, 21% strand | — |
Ligands and binding sites
- GVE · Methyl 4-aminobutanoate · ligand · 2 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains A
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.76 | 0.87 | 64 | empty |
| 2 | 138 | 0.57 | 0.83 | 23 | empty |
| 3 | 63 | 0.36 | 0.79 | 16 | empty |
| 4 | 72 | 0.35 | 0.76 | 15 | empty |
| 5 | 50 | 0.30 | 0.76 | 10 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1520 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 978 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 954 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified, 5 covalent, 1 disulfide (engineered, covalent ligand, additive adduct, disulfide).
Compared structures
- 4I6N · Crystal structure of Trichinella spiralis UCH37 catalytic domain bound to Ubiquitin vinyl… · 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 4I6N · PDBe 4I6N · UniProt P0CG48
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.