Research workbench
Structural basis for the specificity of ubiquitin C- terminal hydrolases
Analyse Structural basis for the specificity of ubiquitin C- terminal hydrolases in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CMX
- Type
- protein
- Length
- 517 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (ubiquitin YUH1-ubal)
- EC
- 3.1.2.15
- UniProt
- P35127, P02248
- Pockets
- 4 · best druggability 0.38
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (ubiquitin YUH1-ubal) (EC 3.1.2.15) | protein | 214 | 36% helix, 22% strand | P35127 |
| B | Protein (ubiquitin YUH1-ubal) (EC 3.1.2.15) | protein | 76 | 20% helix, 36% strand | P02248 |
| C | Protein (ubiquitin YUH1-ubal) (EC 3.1.2.15) | protein | 210 | 36% helix, 21% strand | P35127 |
| D | Protein (ubiquitin YUH1-ubal) (EC 3.1.2.15) | protein | 17 | 0% helix, 35% strand | P02248 |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.38 | 0.76 | 24 | empty |
| 2 | 86 | 0.35 | 0.75 | 21 | empty |
| 3 | 52 | 0.35 | 0.79 | 13 | empty |
| 4 | 67 | 0.33 | 0.76 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1298 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1027 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 711 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 321 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 143 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 1CMX · Structural basis for the specificity of ubiquitin C-terminal hydrolases · the same entry in another collection · chain A against A, TM-score 1.00
- P35127 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase YUH1 (P35127) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P35127
- Every structure of UniProt P02248
- Elsewhere: RCSB PDB 1CMX · PDBe 1CMX · UniProt P35127 · UniProt P02248
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