Research workbench
Structure of ubiquitin activating enzyme (UBA1) in complex with ubiquitin and tak-243
Analyse Structure of ubiquitin activating enzyme (UBA1) in complex with ubiquitin and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TR4
- Type
- protein
- Length
- 2,075 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-activating enzyme E1 1; Ubiquitin
- EC
- 6.2.1.45
- UniProt
- P22515, P0CG53
- Ligands
- 61T
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 972 | 41% helix, 17% strand | P22515 |
| B, D | Ubiquitin | protein | 76 | 24% helix, 34% strand | P0CG53 |
| C | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 951 | 42% helix, 18% strand | P22515 |
Ligands and binding sites
- 61T · [(1~{R},2~{R},3~{S},4~{R})-2,3-bis(oxidanyl)-4-[[2-[3-(trifluoromethylsulfanyl)phenyl]pyrazolo[1,5-a]pyrimidin-7-yl]amino]cyclopentyl]methyl sulfamate · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.78 | 0.80 | 108 | empty |
| 2 | 477 | 0.71 | 0.81 | 66 | empty |
| 3 | 288 | 0.65 | 0.81 | 40 | 61T |
| 4 | 308 | 0.64 | 0.80 | 39 | 61T |
| 5 | 316 | 0.62 | 0.79 | 48 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1603 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1587 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 1461 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5TR4 · Structure of Ubiquitin activating enzyme (Uba1) in complex with ubiquitin and TAK-243 · 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 0.99
- P0CG53 · AlphaFold monomer V2.0 prediction for polyubiquitin-B (P0CG53) · a predicted model of the same protein · chain B 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 P0CG53
- Elsewhere: RCSB PDB 5TR4 · PDBe 5TR4 · UniProt P22515 · UniProt P0CG53
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