Research workbench
Crystal structure of trichinella spiralis UCH37 catalytic domain bound to ubiquitin vinyl methyl ester
Analyse Crystal structure of trichinella spiralis UCH37 catalytic domain bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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