Research workbench
E1 enzyme for ubiquitin like protein activation in complex with ubl
Analyse E1 enzyme for ubiquitin like protein activation in complex with ubl in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H77
- Type
- protein
- Length
- 1,517 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-like modifier-activating enzyme 5; Ubiquitin-fold modifier 1
- UniProt
- Q9GZZ9, P61960
- Ligands
- ATP, MG, ZN
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-like modifier-activating enzyme 5 | protein | 301 | 38% helix, 16% strand | Q9GZZ9 |
| B | Ubiquitin-like modifier-activating enzyme 5 | protein | 302 | 38% helix, 16% strand | Q9GZZ9 |
| C, D | Ubiquitin-like modifier-activating enzyme 5 | protein | 301 | 38% helix, 16% strand | Q9GZZ9 |
| Q, R, S, T | Ubiquitin-fold modifier 1 | protein | 78 | 29% helix, 36% strand | P61960 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 35 copies · chains A, B, T, C, Q, D, R, S
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains C, R, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.81 | 0.82 | 94 | ATP, MG, EDO, PEG |
| 2 | 1057 | 0.80 | 0.82 | 100 | ATP, MG, EDO |
| 3 | 716 | 0.80 | 0.84 | 70 | EDO, PEG |
| 4 | 1041 | 0.80 | 0.81 | 99 | ATP, MG, EDO, PEG |
| 5 | 1058 | 0.80 | 0.81 | 96 | ATP, MG, EDO |
Interfaces
14 interfaces between chains.
- C–D · 3063 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2934 Ų buried · 37 hydrogen bonds · protein-protein
- B–Q · 966 Ų buried · 9 hydrogen bonds · protein-protein
- C–R · 957 Ų buried · 7 hydrogen bonds · protein-protein
- A–T · 945 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6H77 · E1 enzyme for ubiquitin like protein activation in complex with UBL · the same entry in another collection · chain T against T, TM-score 1.00
- Q9GZZ9 · AlphaFold monomer V2.0 prediction for ubiquitin-like modifier- activating enzyme 5… · a predicted model of the same protein · chain C against A, TM-score 1.00
- P61960 · AlphaFold monomer V2.0 prediction for ubiquitin-fold modifier 1 (P61960) · a predicted model of the same protein · chain Q against A, TM-score 0.98
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 Q9GZZ9
- Every structure of UniProt P61960
- Elsewhere: RCSB PDB 6H77 · PDBe 6H77 · UniProt Q9GZZ9 · UniProt P61960
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