MolNFT v1 · #158574 · protein
Crystal structure of ubiquitin E1 (UBA1) in complex with UBC3 (CDC34) and ubiquitin
6NYA · Ubiquitin-activating enzyme E1 1: “Crystal structure of ubiquitin E1 (UBA1) in complex with UBC3 (CDC34) and ubiquitin”. X-ray diffraction, 3 ligands (ATP, MG, SO4), 20 pockets (best druggability 0.79). MolNFT v1 #158574 on…
- 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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