Research workbench
Crystal structure of ubiquitin E1 (UBA1) in complex with UBC3 (CDC34) and ubiquitin
Analyse Crystal structure of ubiquitin E1 (UBA1) in complex with UBC3 (CDC34) and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NYA
- Type
- protein
- Length
- 2,466 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-activating enzyme E1 1; Ubiquitin; Ubiquitin-conjugating enzyme E2-34 kda
- EC
- 6.2.1.45, 2.3.2.23
- UniProt
- P22515, A0A1D6RLC6, P14682
- Ligands
- ATP, MG, SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 987 | 42% helix, 18% strand | P22515 |
| B | Ubiquitin | protein | 78 | 23% helix, 38% strand | A0A1D6RLC6 |
| C | Ubiquitin-conjugating enzyme E2-34 kda (EC 2.3.2.23) | protein | 170 | 30% helix, 17% strand | P14682 |
| D | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 987 | 42% helix, 18% strand | P22515 |
| E | Ubiquitin | protein | 77 | 23% helix, 35% strand | A0A1D6RLC6 |
| F | Ubiquitin-conjugating enzyme E2-34 kda (EC 2.3.2.23) | protein | 167 | 32% helix, 17% strand | P14682 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B, D, E
- MG · Magnesium ion · metal · 2 copies · chains A, D
- SO4 · Sulfate ion · ion · 15 copies · chains A, D
- EDO · 1,2-ethanediol · additive · 21 copies · chains A, B, D, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.79 | 0.87 | 54 | SO4 |
| 2 | 328 | 0.75 | 0.87 | 39 | EDO |
| 3 | 441 | 0.71 | 0.82 | 46 | empty |
| 4 | 838 | 0.71 | 0.77 | 55 | empty |
| 5 | 244 | 0.70 | 0.86 | 44 | empty |
Interfaces
9 interfaces between chains.
- A–D · 2020 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1841 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 1784 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 1741 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1698 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6NYA · Crystal Structure of ubiquitin E1 (Uba1) in complex with Ubc3 (Cdc34) and ubiquitin · the same entry in another collection · chain F against F, 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 D against A, TM-score 0.99
- P14682 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2-34 kda (P14682) · a predicted model of the same protein · chain F 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 P22515
- Every structure of UniProt A0A1D6RLC6
- Every structure of UniProt P14682
- Elsewhere: RCSB PDB 6NYA · PDBe 6NYA · UniProt P22515 · UniProt A0A1D6RLC6 · UniProt P14682
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