MolNFT v1 · #101319 · protein
Crystal structure of UBA1 in complex with ubiquitin-AMP and thioesterified ubiquitin
4NNJ · Ubiquitin-activating enzyme E1 1: “Crystal structure of UBA1 in complex with ubiquitin-AMP and thioesterified ubiquitin”. X-ray diffraction, 2 ligands (AMP, SO4), 20 pockets (best druggability 0.77). MolNFT v1 #101319 on GenesisL1…
- PDB
- 4NNJ
- Type
- protein
- Length
- 2,244 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-activating enzyme E1 1; UBA1
- UniProt
- P22515, P0CG63
- Ligands
- AMP, SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ubiquitin-activating enzyme E1 1 | protein | 1006 | 42% helix, 17% strand | P22515 |
| B | UBA1 | protein | 78 | 23% helix, 38% strand | P0CG63 |
| D, E | UBA1 | protein | 77 | 23% helix, 32% strand | P0CG63 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, D, E
- GOL · Glycerol · additive · 29 copies · chains A, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 788 | 0.77 | 0.81 | 85 | empty |
| 2 | 463 | 0.74 | 0.83 | 63 | empty |
| 3 | 61 | 0.73 | 0.98 | 23 | GOL |
| 4 | 350 | 0.70 | 0.83 | 47 | empty |
| 5 | 325 | 0.68 | 0.83 | 53 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1887 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1649 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1638 Ų buried · 33 hydrogen bonds · protein-protein
- C–E · 953 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 34 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4NNJ · Crystal structure of Uba1 in complex with ubiquitin-AMP and thioesterified ubiquitin · the same entry in another collection · chain E against E, 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 0.99
- P0CG63 · AlphaFold monomer V2.0 prediction for polyubiquitin (P0CG63) · a predicted model of the same protein · chain D against A, TM-score 0.90
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 P0CG63
- Elsewhere: RCSB PDB 4NNJ · PDBe 4NNJ · UniProt P22515 · UniProt P0CG63
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