MolNFT v1 · #171824 · protein
UBA1 bound to two E2 (UBC13) molecules
6ZHS · Ubiquitin-activating enzyme E1 1: “UBA1 bound to two E2 (UBC13) molecules”. X-ray diffraction, 1 ligand (SO4), 19 pockets (best druggability 0.84). MolNFT v1 #171824 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZHS
- Type
- protein
- Length
- 1,297 residues
- Chains
- 3
- 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
- SO4
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 994 | 42% helix, 17% strand | P22515 |
| B | Ubiquitin-conjugating enzyme E2 13 (EC 2.3.2.23) | protein | 152 | 34% helix, 17% strand | P52490 |
| C | Ubiquitin-conjugating enzyme E2 13 (EC 2.3.2.23) | protein | 151 | 33% helix, 18% strand | P52490 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.84 | 0.85 | 104 | empty |
| 2 | 873 | 0.70 | 0.75 | 69 | empty |
| 3 | 50 | 0.68 | 0.97 | 22 | GOL |
| 4 | 605 | 0.68 | 0.78 | 61 | GOL |
| 5 | 211 | 0.66 | 0.85 | 42 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 1957 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1290 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 55 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6ZHS · Uba1 bound to two E2 (Ubc13) molecules · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.98
- 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 6ZHS · PDBe 6ZHS · UniProt P22515 · UniProt P52490
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