Research workbench
UBA1-UBC13 disulfide mediated complex
Analyse UBA1-UBC13 disulfide mediated complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZHT
- Type
- protein
- Length
- 1,136 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-activating enzyme E1 1; Ubiquitin-conjugating enzyme E2 13
- EC
- 6.2.1.45, 2.3.2.23
- UniProt
- P22515, P52490
- Ligands
- CL
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 983 | 42% helix, 17% strand | P22515 |
| B | Ubiquitin-conjugating enzyme E2 13 (EC 2.3.2.23) | protein | 153 | 33% helix, 22% strand | P52490 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 837 | 0.79 | 0.82 | 91 | CL |
| 2 | 661 | 0.77 | 0.82 | 64 | GOL |
| 3 | 428 | 0.69 | 0.80 | 50 | empty |
| 4 | 704 | 0.66 | 0.75 | 64 | empty |
| 5 | 390 | 0.59 | 0.76 | 48 | GOL, CL |
Interfaces
1 interface between chains.
- C–B · 1902 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6ZHT · Uba1-Ubc13 disulfide mediated complex · the same entry in another collection · chain C against C, TM-score 1.00
- P22515 · AlphaFold monomer V2.0 prediction for ubiquitin-activating enzyme E1 1 (P22515) · a predicted model of the same protein · chain C against A, TM-score 0.95
- P52490 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 13 (P52490) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P52490
- Elsewhere: RCSB PDB 6ZHT · PDBe 6ZHT · UniProt P22515 · UniProt P52490
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