Research workbench
Yeast UBA1 in complex with UBC3 and ATP
Analyse Yeast UBA1 in complex with UBC3 and ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZHU
- Type
- protein
- Length
- 4,681 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2-34 kda; Ubiquitin-activating enzyme E1 1
- EC
- 2.3.2.23, 6.2.1.45
- UniProt
- P14682, P22515
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Ubiquitin-conjugating enzyme E2-34 kda (EC 2.3.2.23) | protein | 177 | 31% helix, 14% strand | P14682 |
| F, H | Ubiquitin-conjugating enzyme E2-34 kda (EC 2.3.2.23) | protein | 178 | 28% helix, 15% strand | P14682 |
| D | Ubiquitin-conjugating enzyme E2-34 kda (EC 2.3.2.23) | protein | 173 | 31% helix, 16% strand | P14682 |
| A, C | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 995 | 42% helix, 17% strand | P22515 |
| E | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 993 | 42% helix, 17% strand | P22515 |
| G | Ubiquitin-activating enzyme E1 1 (EC 6.2.1.45) | protein | 992 | 41% helix, 17% strand | P22515 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, E, C, G
- MG · Magnesium ion · metal · 4 copies · chains A, E, C, G
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 | 917 | 0.83 | 0.85 | 87 | empty |
| 2 | 1094 | 0.82 | 0.83 | 133 | empty |
| 3 | 1109 | 0.82 | 0.83 | 101 | empty |
| 4 | 703 | 0.79 | 0.84 | 69 | empty |
| 5 | 634 | 0.79 | 0.84 | 58 | empty |
Interfaces
10 interfaces between chains.
- H–G · 2299 Ų buried · 19 hydrogen bonds · protein-protein
- F–E · 2228 Ų buried · 18 hydrogen bonds · protein-protein
- B–A · 2158 Ų buried · 18 hydrogen bonds · protein-protein
- D–C · 2055 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1966 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6ZHU · Yeast Uba1 in complex with Ubc3 and ATP · the same entry in another collection · chain G against G, 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
- P14682 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2-34 kda (P14682) · a predicted model of the same protein · chain D against A, TM-score 0.91
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 P14682
- Every structure of UniProt P22515
- Elsewhere: RCSB PDB 6ZHU · PDBe 6ZHU · UniProt P14682 · UniProt P22515
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