Research workbench
Crystal structure of human ubiquitin activating enzyme E1 (UBA1) in complex with ubiquitin
Analyse Crystal structure of human ubiquitin activating enzyme E1 (UBA1) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DC6
- Type
- protein
- Length
- 2,140 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-like modifier-activating enzyme 1; Ubiquitin
- EC
- 6.2.1.45
- UniProt
- P22314, P62979
- Ligands
- POP, MG
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-like modifier-activating enzyme 1 (EC 6.2.1.45) | protein | 992 | 38% helix, 18% strand | P22314 |
| B, D | Ubiquitin | protein | 76 | 16% helix, 33% strand | P62979 |
| C | Ubiquitin-like modifier-activating enzyme 1 (EC 6.2.1.45) | protein | 996 | 39% helix, 17% strand | P22314 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 895 | 0.74 | 0.78 | 77 | empty |
| 2 | 868 | 0.73 | 0.77 | 88 | empty |
| 3 | 800 | 0.69 | 0.76 | 59 | empty |
| 4 | 350 | 0.64 | 0.80 | 40 | MG, POP |
| 5 | 502 | 0.63 | 0.76 | 45 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1626 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1624 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 1020 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6DC6 · Crystal structure of human ubiquitin activating enzyme E1 (Uba1) in complex with ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
- P22314 · AlphaFold monomer V2.0 prediction for ubiquitin-like modifier- activating enzyme 1… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P22314
- Every structure of UniProt P62979
- Elsewhere: RCSB PDB 6DC6 · PDBe 6DC6 · UniProt P22314 · UniProt P62979
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