MolNFT v1 · #15655 · protein
Crystal structure of a ubp-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde
1NBF · Ubiquitin carboxyl-terminal hydrolase 7: “Crystal structure of a ubp-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde”. X-ray diffraction, 14 pockets (best druggability 0.73). MolNFT v1 #15655 on…
- PDB
- 1NBF
- Type
- protein
- Length
- 1,186 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin carboxyl-terminal hydrolase 7; Ubiquitin aldehyde
- EC
- 3.1.2.15
- UniProt
- Q93009, P62988
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.1.2.15) | protein | 347 | 31% helix, 29% strand | Q93009 |
| C, D | Ubiquitin aldehyde | protein | 76 | 20% helix, 32% strand | P62988 |
| E | Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.1.2.15) | protein | 340 | 29% helix, 23% strand | Q93009 |
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 592 | 0.73 | 0.81 | 61 | empty |
| 2 | 520 | 0.71 | 0.81 | 61 | empty |
| 3 | 302 | 0.67 | 0.82 | 37 | empty |
| 4 | 144 | 0.50 | 0.79 | 25 | empty |
| 5 | 113 | 0.49 | 0.80 | 13 | empty |
Interfaces
8 interfaces between chains.
- B–C · 1899 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 1866 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 632 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 287 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 175 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 1NBF · Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex… · 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 Q93009
- Every structure of UniProt P62988
- Elsewhere: RCSB PDB 1NBF · PDBe 1NBF · UniProt Q93009 · UniProt P62988
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.