Research workbench
Yeast UBA1 in complex with ubiquitin
Analyse Yeast UBA1 in complex with ubiquitin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZQH
- Type
- protein
- Length
- 2,163 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-activating enzyme E1 1; Ubiquitin-40S ribosomal protein S31
- EC
- 6.2.1.45
- UniProt
- P22515, P05759
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 1005 | 42% helix, 17% strand | P22515 |
| B, D | Ubiquitin-40S ribosomal protein S31 | protein | 76 | 24% helix, 33% strand | P05759 |
| C | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 1006 | 42% helix, 17% strand | P22515 |
Ligands and binding sites
- BME · Beta-mercaptoethanol · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, C
- PG4 · Tetraethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.69 | 0.81 | 47 | empty |
| 2 | 295 | 0.69 | 0.83 | 49 | empty |
| 3 | 250 | 0.65 | 0.82 | 37 | empty |
| 4 | 231 | 0.65 | 0.83 | 37 | empty |
| 5 | 280 | 0.63 | 0.81 | 43 | GOL |
Interfaces
3 interfaces between chains.
- A–C · 1785 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1684 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 1680 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
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 P22515
- Every structure of UniProt P05759
- Elsewhere: RCSB PDB 6ZQH · PDBe 6ZQH · UniProt P22515 · UniProt P05759
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